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Head and neck cancers are among the most prevalent cancers in the body. The aim of this study was to evaluate the expression of P16 and Epstein-Barr virus/latent membrane protein (EBV/LMP1) markers by immunohistochemistry in patients with squamous cell carcinoma of the head and neck.In this study, all tissue samples of head and neck biopsies from 75 patients with confirmed diagnosis of squamous cell carcinoma (HNSCC) during 2016 to 2018 who admitted to the pathology laboratory of Imam Khomeini Hospital, Iran were selected. Paraffin blocks which prepared from these tissue samples were obtained. The slides were prepared from all samples for routine Hematoxylin-Eosin and immunohistochemical staining to evaluate the expression of EBV/LMP1 and P16 markers in cancer cells.The mean age of patients was 63 years and most patients (85.3%) were male in 75 patients with HNSCC. There was a significant relationship between EBV/LMP1 biomarker expression and vascular invasion in patients (p 0.05). There was no relationship between EBV/LMP1 biomarker expression and age, sex ,anatomical site of tumor and tumor differentiation of patients (p 0.05). There was no relationship between P16 biomarker expression and age, sex, tumor differentiation, anatomical site of tumor and vascular invasion of patients (p 0.05). There is a significant relationship between P16 biomarker and EBV/LMP1 biomarker staining (p 0.05).The level of P16 positive biomarker was high in patients with HNSCC. However, the EBV/LMP1 positive biomarker was moderate in patients. There was a relationship between EBV/LMP1 biomarker expression and vascular invasion in HNSCC patients, as well as between P16 biomarker and EBV/LMP1 biomarker staining.

Neisseria meningitidis is one of the most important causes of meningitis and pathogens-associated deaths in developing and developed countries. Effective anti-microbial agents are pivotal to treat and control N. meningitidis infections. The aim of the present study was to systematically review published studies on the antibiotic resistance of N. meningitidis in the last 20 years (2000-2020) in the world.Published researches were identified through a literature search using reputable databases including PubMed, Scopus, and Web of Science. Finally, 24 studies were included for a random-effects model meta-analysis.The overall resistance to most commonly used antibiotics such as ceftriaxone, cefotaxime, ciprofloxacin and rifampin was low, ranging from 1 to 3.4%. However, non-sensitivity to penicillin, as the first-line antibiotic against N. meningitidis, was higher (27.2%). Altogether, the resistance to the first-line antibiotics (except penicillin) is still low indicating these drugs are effective against meningococcal meningitis. We also found a significant gap between MIC and disk diffusion for evaluating resistance to antibiotics in which disk diffusion overestimate the resistance rate.To properly management and prevent the spread of N. miningitidis isolates resistant antibiotics, it is necessary to monitor the pattern of antibiotic susceptibility regionally and globally using the MIC methods.

Klebsiella pneumoniae is one of the major causes of nosocomial infections worldwide which can cause several diseases in children and adults. The globally dissemination of hyper-virulent strains of K. pneumoniae and the emergence of antibiotics-resistant isolates of this pathogen narrows down the treatment options and has renewed interest in its vaccines. Vaccine candidates of Klebsiella pneumoniae have not been adequately protective, safe and globally available yet. In K. pneumoniae infection, it is well known that B cells that induce robust humoral immunity are necessary for the host complete protection. Identifying the B cell epitopes of antigens is valuable to design novel vaccine candidates. In the present study using immunoinformatics approaches we found B cell epitopes of four K. pneumoniae type 1 fimbriae antigens namely FimA, FimF, FimG, and FimH. Linear and conformational B cell epitopes of each antigen were predicted using different programs. Subsequently, many bioinformatics assays were applied to choose the best epitopes including prediction antigenicity, toxicity, human similarity and investigation on experimental records. These assays resulted in final four epitopes (each for one Fim protein). These final epitopes were modeled and their physiochemical properties were estimated to be used as potential vaccine candidates. Altogether, we found four B cell epitopes of K. pneumoniae Fim antigens that are immunogen, antigenic, not similar to human peptides, not allergen and not toxic. Also, they have suitable physiochemical properties to administrate as vaccine, although their complete efficacy should be also shown in vitro and in vivo.

Klebsiella pneumoniae (K. pneumoniae) is a causative agent of severe infections in humans. There is no publically available vaccine for K. pneumoniae infections yet. Here, using comprehensive immun...

Objective Current therapy strategies of leishmaniasis have some problems such as high cost, toxicity and side effects. Plant extracts can be a source of drugs to control leishmaniasis. In this study, the effect of hydroalcoholic and chloroformic extracts of Vigna radiata, Tamarix ramosissima, and Carthamus lanatus on Leishmania major and L. tropica was studied. Methods The plant samples were collected from west of Iran and their extracts were prepared. Anti-promastigote activity assay of all extracts was done using tetrazolium-dye assay. Results Only high concentrations of V. radiata and C. lanatus were able to inhibit Leishmania, while both high and low concentrations of T. ramosissima had antileishmanial effect. No difference was observed between hydroalcoholic with chloroformic extract of each plant. Conclusion Altogether, the results revealed the antileishmanial activity of T. ramosissima extracts against L. major and L. tropica, indicating its potential as an antileishmanial agent.

Introduction: Accurate evaluation of the survival rate among HIV-positive populations is pivotal for HIV management. Objective: This study aimed to investigate the survival rate and potential survival-related factors in HIV/AIDS patients from 2011 to 2019 in the city of Kermanshah in the west of Iran. Method: In this study, 915 HIV-positive patients registered by the Kermanshah Behavioral diseases counseling center, were surveyed from 2011 to 2019. By reading the patients' files, the proper data related to the survival factors were extracted and statistically analyzed. Results: Of 915 patients, 220 (24%) died. The one-year, five-year, and ten-year survival rates were 84%, 72%, and 62%, respectively. There was a significant relationship between the survival rate and many other parameters, including treatment variables, CD4+ T cell count, the way of HIV transmission, level of education, gender, and marital status. Over time, timely initiation of treatment has increased. The data also showed that HIV transmission through drug injection has decreased, while the sexual transmission of HIV has increased. Conclusions: The results showed that in recent years, due to the appropriate treatment, the survival rate of HIV patients has increased. The highest risk factor of death was for people with low CD4+ T cell count, lack of antiretroviral therapy, low level of education, male gender, and people who inject drugs. These people need more attention to get tested for HIV- related indexes and to receive proper treatment.

Klebsiella pneumoniae is one of the major causes of nosocomial infections worldwide which can cause several diseases in children and adults. The globally dissemination of hyper-virulent strains of K. pneumoniae and the emergence of antibiotics-resistant isolates of this pathogen narrows down the treatment options and has renewed interest in its vaccines. Vaccine candidates of Klebsiella pneumoniae have not been adequately protective, safe and globally available yet. In K. pneumoniae infection, it is well known that B cells that induce robust humoral immunity are necessary for the host complete protection. Identifying the B cell epitopes of antigens is valuable to design novel vaccine candidates. In the present study using immunoinformatics approaches we found B cell epitopes of four K. pneumoniae type 1 fimbriae antigens namely FimA, FimF, FimG, and FimH. Linear and conformational B cell epitopes of each antigen were predicted using different programs. Subsequently, many bioinformatics assays were applied to choose the best epitopes including prediction antigenicity, toxicity, human similarity and investigation on experimental records. These assays resulted in final four epitopes (each for one Fim protein). These final epitopes were modeled and their physiochemical properties were estimated to be used as potential vaccine candidates. Altogether, we found four B cell epitopes of K. pneumoniae Fim antigens that are immunogen, antigenic, not similar to human peptides, not allergen and not toxic. Also, they have suitable physiochemical properties to administrate as vaccine, although their complete efficacy should be also shown in vitro and in vivo. Electronic supplementary material The online version of this article (10.1007/s10989-020-10134-3) contains supplementary material, which is available to authorized users.

Context: Sepsis is one of the most common causes of neonatal mortality, especially in developing countries. The purpose of this study was to systematically review the bacterial causative agents of neonatal sepsis and their antibiotic susceptibility in Iran. Material and Methods: We searched all previously published papers to gather related information on Iranian neonatal sepsis in international and national databases (in both Persian and English) from 2006 to 2018. The standard STROBE checklist was used for quality assessment. The data were analyzed by statistical methods with a random-effects model using Stata 14 software. Results: A total of 89,472 neonates with sepsis (presented in 17 studies) were included in this systematic review. The mortality rate of neonates was 28.0%. The proportions of neonatal sepsis caused by Gram-negative and Gram-positive bacteria were 66.0% and 33.0%, respectively. The most common bacteria causing neonatal sepsis were Klebsiella pneumoniae and Pseudomonas aeruginosa (Gram-negative) and coagulase-negative staphylococci and Staphylococcus aureus (Gram-positive). Conclusions: Gram-negative bacteria are the most common causes of neonatal sepsis in Iran. Imipenem is the most effective antibiotic against Gram-negative bacilli and vancomycin against Gram-positive cocci causing neonatal sepsis in Iran.

Current therapy strategies of leishmaniasis have some problems such as high cost, toxicity and side effects. Plant extracts can be a source of drugs to control leishmaniasis. In this study, the effect of hydroalcoholic and chloroformic extracts ofThe plant samples were collected from west of Iran and their extracts were prepared. Anti-promastigote activity assay of all extracts was done using tetrazolium-dye assay.Only high concentrations ofAltogether, the results revealed the antileishmanial activity of

Introduction: Urinary Tract Infection (UTI) is one of the most common bacterial infections and Escherichia coli is the most common organism that causes UTI. However, the incidence of community acquired UTI caused by Extended spectrum betalactamase (ESBL)-producing strains of E.coli, in particular CTX-M genes, is on the rise worldwide. Aim: To detect the frequency of CTX-M gene subgroups in uropathogenic E.coli. Materials and Methods: In this descriptive-analytical study, 240 isolates of E. coli were studied. All isolates were isolated from UTIs in Kermanshah University of Medical Sciences, Kermanshah, Iran, in 2014 to 2015. After screening for ESBL, the CTX-M, CTX-M-2, CTX-M-8, CTX-M-25 and CTX-M-3 genes were detected among ESBL- producing isolates using PCR. Results: Of the 240 E. coli isolates, 67 were ESBL-producing isolates. Sixty one isolates (91%) contained CTX-M gene, of which 57 (85%), 3 (4.5%), 3 (4.5%) and 1(1.49%) contained CTXM-3, CTX-M-8, CTX- M-25 and CTX-M-2, respectively. Conclusion: Due to the high resistance of E. coli to betalactam drugs in this region, these drugs have limited effects for treatment of UTI in outpatient. The frequency of CTX-M-2, CTX-M-8, CTX-M-25 beta-lactamases in isolates of E. coli is relatively low but the overall prevalence of CTX-M and CTXM-3 beta-lactamases is high which indicates the spread of drug resistance.

Background: Integron is an important element in creating multi-drug resistant (MDR) bacteria. This study evaluated the relationship of class I integron and antibiotic resistance in extended-spectrum beta-lactamase producing (ESBL) isolates of Escherichia coli (E. coli). Methods: A total of 66 ESBL-producing E. coli were isolated from urinary tract infection in Kermanshah and their antimicrobial susceptibility was assessed. The incidence of class I integron was determined in isolates using PCR. The class I integron-associated gene cassettes were also verified by DNA sequencing. Data were analyzed using statistical methods. Results: Of 66 ESBL-producing isolates, 65 (98.5%) were MDR. The most prevalent antibiotic resistance of the isolates was observed for ampicillin (98.4%), ceftriaxone (98.4%), cefotaxime (95.4%), and co-trimoxazole (86.3%). The frequency of class I integron in isolates was 92.3%. The relationship between class I integron and resistance to streptomycin, co-trimoxazole, and ceftazidime was statistically significant. The genes encoding resistance to streptomycin and co-trimoxazole, as well as a gene encoding a protein with unknown function, were associated with class I integron. The most common gene cassette was dfrA17-aadA5. Conclusions: The results indicate a high prevalence of antibiotic resistance among ESBL-producing isolates to the antibiotics commonly used for the empirical treatment of urinary tract infections. The frequency of class I integron and associated gene cassettes involving resistance to antibiotics is high. There is a high percentage of MDR among the ESBL-producing isolates, which mostly contain gene cassettes. These findings suggest a strong association of integron and ESBL genes in the isolates.

Background: The changes of platelet parameters can be a useful index for rapid diagnosis of urinary tract infection (UTI), since platelet changes are routinely determined through complete blood count (CBC) test. The correlation between platelet indices, included number (PLTs), mean platelet volume (MPV) and platelet distribution width (PDW), which are the indicators of production and function of platelets, with UTI was evaluated in this study. Materials and Methods: In this descriptive-analytical study, 97 patients with UTI (patient group) and 117 healthy people (control group). The average age for the patient and the control group was 10.84±6.68 and 11.34±7.1 years old, respectively. This study was done during 2016-2018 in Imam Reza Hospital, Kermanshah, west of Iran. The PLT, MPV, PDW, and other inflammatory indices, including white blood cell, neutrophils, lymphocytes, erythrocyte sedimentation rate (ESR), and C-reactive protein (CRP) were evaluated. The diagnosis of bacteria was done using routine microbiological and biochemical methods. The platelet indices were statistically compared between the patients and the control groups (T test and Chi square test). Results: The most common isolated gram negative and gram positive bacteria were E. coli, Citrobacter, and Staphylococcus aureus, respectively. In the patient group, PLT number was significantly higher than that in the control group (p=0.0007), while difference of other indices such as MPV, PDW, neutrophils, lymphocytes, CRP, and ESR were not statistically significant between the two groups. In case of UTI with gram positive bacteria, PLT number (p=0.05) was lower but MPV (p=0.02) and PDW (p=0.045) was higher compared to the UTI with gram negative bacteria. Conclusion: The results of this study showed that the platelet number could be a useful diagnostic index for urinary tract infection. However, more studies need to be done with higher number of patients to evaluate the more details of platelet changes during UTIs.

Background: Klebsiella pneumoniae is one of the important opportunistic pathogens causing serious infections, both community and hospital-acquired, with high resistance to antibiotics. Objectives: We aimed to determine the molecular typing of K. pneumoniae isolates using pulse field gel electrophoresis (PFGE). Methods: Sixty-two consecutive non-duplicate K. pneumoniae isolates were isolated from clinical specimens in three hospitals of Kermanshah, west of Iran. A total of K. pneumoniae was confirmed by API-20E kit. Antibiotic susceptibility testing and ESBL screening were performed following the genotyping of isolates using PFGE. The pattern of DNA bands was examined by the 6.6 version of the Gelcompar II (Applied Maths, Belgium). The calculation of similarities was done by the Dice coefficient, and the unweighted paired group method was used for cluster analysis (UPGMA). Results: Fifty-eight percent of isolates were phenotypically ESBL positive. Twenty-nine pulsotypes (X1-29) were determined with various genotype patterns. Four clones (including 18 isolates) showed a close genetic relationship and were from ICU, burn and infectious wards in one hospital. Pulsotypes X15 to X29, each presented a unique genotype and the majority of these strains (> 50%) were from the emergency ward. Four isolates were non-typable. Conclusions: Our results indicate the genotypic variation of K. pneumoniae isolates, which may suggest the different origins for isolates, as well as ongoing changes of bacterial genome. However, the presence of the isolates with similar genotype may show a common origin and consequently, the dissemination of strains in hospital wards, especially in ICU and burn wards. Therefore, Kermanshah hospitals need to establish an effective infectious control system to manage and monitor the spread of resistant strains.

Background: Fluoroquinolones have been used for empirical treatment of urinary tract infections in recent years. This study aimed at identifying mutations in gyrA and parC genes and their correlation with fluoroquinolone minimal inhibitory concentration (MIC) among extended-spectrum β-lactamase-producing (ESBL) Escherichia coli. Methods: A total of 240 E. coli were isolated from urine of patients during 2014 and 2015 in the west of Iran. The isolates were screened for ESBL-producing phenotype using combined disc diffusion test. The susceptibility of ESBL isolates to ciprofloxacin and levofloxacin was determined by disk diffusion and microdilution assay. PCR, sequencing and bioinformatics analysis were performed to identify mutations in gyrA and parC genes. Results: Of 240 isolates, 66 (27.5%) were ESBL positive. Of them, 45 (68.1%) isolates were resistant to both ciprofloxacin and levofloxacin. Sequence analysis showed mutations in the quinolone resistance determining region (QRDR) in the 2 codons (Ser-83, Asp-87) of gyrA and 2 codons (Ser-80, Glu-84) of parC. One mutation at codon of Ala-192 was found outside the QRDR in parC. Conclusions: Isolates with mutations in QRDR of parC and gyrA had the higher MIC level compared to isolates with mutations only in gyrA. The highest level of resistance was detected in isolates with accumulation of mutations in gyrA and parC. A high frequency of fluoroquinolone resistance among ESBL producing E. coli isolates indicated the clustered transmission of resistance genes in this bacterium. A new mutation outside the QRDR of parC was detected, which may play a role in fluoroquinolone resistance.

Background and Objective: Aminoglycoside resistance genes have been disseminated among gram negative bacilli such as Citrobacter. This study aimed to determine aminoglycoside resistance and the frequency of aac (3) -IIa, aac (3) -IV, aac (6 ') - Ib, aph (3') -Ia and ant (2")-Ia genes among Citrobacter isolates. Methods: One hundred clinical isolates of Citrobacter were identified using the API-20E. Isolates resistant to gentamicin and tobramycin were identified using Disk diffusion method. After extracting the bacterial genome, the presence of aac (3)-IIa, aac (3)-IV, aac (6 ')-Ib, aph (3')-Ia and ant (2")-Ia genes was tested by PCR. The data were analyzed using statistical methods. Results: Of 100 isolates , 77 % were Citrobacter ferundii and the rest was C.koseri, C.braakii and C.youngae with 13 % , 9 % and 1 %, respectively. Twenty seven isolates were resistant to gentamicin and/or tobramycin. Frequency of aac (6') -Ib, aph (3') -Ia and ant (2")-Ia was 70.3 %, 62.9 % and 25.9 %, respectively. But aac (3)-IIa and aac (3)-IV genes were not found in any of the isolates. Conclusion: C. ferundii is the most common Citrobacter species among hospitalized patients in Kermanshah and highly resistant to gentamicin and tobramycin. The high prevalence of aac (6') -Ib, aph (3') -Ia and ant (2")-Ia genes causing resistance to aminoglycosides in Citrobacter species in our study. However, this high prevalence of resistance genes may be the consequence of inappropriate prescribing of antibiotics and the lack of appropriate infection control measures in hospitals.

Background: Klebsiella pneumoniae causes a variety of infections including community acquired pneumonia and nosocomial infections. Objectives: The aim of this study was to determine the plasmid-associated quinolone-resistance (PMQR) genes and mutations in quinolone-resistance determining region (QRDR) of topoisomerase genes in K. pneumoniae. Methods: One hundred clinical K. pneumoniae isolates were collected from Kermanshah hospitals for this study. The minimum inhibitory concentrations (MIC) for levofloxacin and ciprofloxacin was determined by broth microdilution method. The presence of PMQR genes (qnrA, qnrB, qnrS, aac (6´)-Ib, and qepA) among isolates resistant to fluoroquinolones was detected by PCR. All PCR products for topoisomerase genes (gyrA, gyrB and parC) were sequenced and analyzed. Results: Sequence analysis showed mutations in gyrA at codons 83 and 87 in 24 (85.7%) and 20 (71.4%) of isolates, respectively. For parC mutations were detected at codons 80 and 84 in 15 (53.6%) and 7 (25%) isolates, respectively. At the outside of QRDR in gyrA and gyrB, mutations were also observed. The mutation was not detected in the QRDR of gyrB. The qnrB, qnrS, and aac (6')-Ib-cr were found in 1 (3.6%), 11 (39.3%) and 25 (89.3%) of isolates, respectively. Howevr, the qnrA and qepA genes were not detected among isolates. Conclusions: The resistance to fluoroquinolones is relatively high among K. pneumonia and mutations in QRDR of topoisomerase genes play an important role for this resistance. The plasmid-mediated genes also increase the level of resistance. The mutations outside the QRDR of topoisomerase genes also occur, but their exact role in resistance needs to be clarified.