Prevalence of human metapnemovirus in children with acute respiratory tract infection Shiraz, Iran during 2014-2015

Background: Human metapneumovirus (HMPV) is a newly discovered viral agent of respiratory infections. In present study we determined prevalence of HMPV in children less than10 years with acute respiratory infections (ARTI) that referred to the health centers of Shiraz University of Medical Sciences, Iran.Methods: Nasal swabs were obtained from 180 children less than 10 years old with respiratory tract symptoms during fall, winter and spring seasons of 2014 and 2015. The specimens were tested for HMPV F gene using one step RT-PCR.Results: HMPV was detected in 30 (16.66%) of 180 children with (ARTI) less than 10 years old. Approximately 63.33% of HMPV positive patients aged less than 3 years and 86.33% were younger than 5 years old. The clinical symptoms were bronchiolitis, wheezing and cough.Conclusions: The frequency distribution of HMPV revealed that most patients aged between 1 to 5 years and this virus is one of the respiratory viral agents to causes ATRI, especially children less than 5 years old

The Very Low Frequency of Epstein-Barr JC and BK Viruses DNA in Colorectal Cancer Tissues in Shiraz, Southwest Iran

Viruses including Epstein-Barr virus (EBV), JCV and BKV have been reported to be associated with some cancers. The association of these viruses with colorectal cancers remains controversial. Our objective was to investigate their infections association with adenocarcinoma and adenomatous polyps of the colon. Totally, 210 paraffin-embedded tissue specimens encompassing 70 colorectal adenocarcinoma, 70 colorectal adenomatous and 70 colorectal normal tissues were included. The total DNA was extracted, then qualified samples introduced to polymerase chain reaction (PCR). The EBV, JCV and BKV genome sequences were detected using specific primers by 3 different in-house PCR assays. Out of 210 subjects, 98 cases were female and the rest were male. The mean age of the participants was 52 ± 1.64 years. EBV and JCV DNA was detected just in one (1.42%) out of seventy adenocarcinoma colorectal tissues. All adenomatous polyp and normal colorectal tissues were negative for EBV and JCV DNA sequences. Moreover, all the patients and healthy subjects were negative for BKV DNA sequences. The results suggested that EBV and JCV genomes were not detectable in the colorectal tissue of patients with colorectal cancer in our population. Hence, BKV might not be necessitated for the development of colorectal cancer. The findings merit more investigations

Genetic variations of OprD porin protein in imipenem resistant clinical isolates of Pseudomonas aeruginosa in burn patients

Background: Drug resistance is one of the important threats in uncontrolled infections by Pseudomonas aeruginosa, an opportunistic nosocomial pathogen, in burn patients. The presence of OprD porin protein in the bacterial cell wall is one of the mechanisms for resistance against hydrophilic drugs in this bacterium. Objective: The aim of this study was to evaluate genetic sequence rearrangements of OprD gene in imipenem resistant clinical isolates of pseudomonas aeruginosa in burn patients. Methods: This cross sectional study was performed in Ghotbeddin Shirazi Hospital from October 2013 to February 2015. A total of 253 wound samples were evaluated for Pseudomonas aeruginosa. All isolates were evaluated using specific sequencing of the target region. Genetic sequence rearrangements were compared with the sensitivity pattern of the isolates to the imipenem. Findings: Pseudomonas aeruginosa was found in 22% of the samples in Shiraz burn center. More than 90% of the isolates were multi drug resistant while only 25% were sensitive to imipenem. More than 80% of the imipenem resistant isolates had rearrangement in the gene associated with OprD protein. Conclusion: With regards to the results, it seems that Pseudomonas aeruginosa, as a prevalent microorganism in burn wounds, has rearrangement in the gene associated with OprD porin protein. This rearrangement may play a role in drug resistance of the Pseudomonas aeruginosa isolates in hospitalized patients. Keywords: Burns, Pseudomonas Aeruginosa, Imipenem, OprD Protei

Prevalence of underlying diseases in hospitalized patients with COVID-19: a systematic review and meta-analysis.

Introduction In the beginning of 2020, an unexpected outbreak due to a new corona virus made the headlines all over the world. Exponential growth in the number of those affected makes this virus such a threat. The current meta-analysis aimed to estimate the prevalence of underlying disorders in hospitalized COVID-19 patients. Methods A comprehensive systematic search was performed on PubMed, Scopus, Web of science, and Google scholar, to find articles published until 15 February 2020. All relevant articles that reported clinical characteristics and epidemiological information of hospitalized COVID-19 patients were included in the analysis. Results The data of 76993 patients presented in 10 articles were included in this study. According to the meta-analysis, the pooled prevalence of hypertension, cardiovascular disease, smoking history and diabetes in people infected with SARS-CoV-2 were estimated as 16.37% (95%CI: 10.15%-23.65%), 12.11% (95%CI 4.40%-22.75%), 7.63% (95%CI 3.83%-12.43%) and 7.87% (95%CI 6.57%-9.28%), respectively. Conclusion According to the findings of the present study, hypertension, cardiovascular diseases, diabetes mellitus, smoking, chronic obstructive pulmonary disease (COPD), malignancy, and chronic kidney disease were among the most prevalent underlying diseases among hospitalized COVID-19 patients, respectively

Bioinformatics and Structural Analysis of Antigenic Variation in the Hemagglutinin Gene of the Influenza A(H1N1)pdm09 Virus Circulating in Shiraz (2013 to 2015)

ABSTRACT Circulating influenza A virus provided an excellent opportunity to study the adaptation of the influenza A(H1N1)pdm09 virus to the human host. Particularly, due to the availability of sequences taken from isolates, we could monitor amino acid changes and the stability of mutations that occurred in hemagglutinin (HA). HA is crucial to viral infection because it binds to ciliated cell receptors and mediates the fusion of cells and viral membranes; because antibodies that bind to HA may block virus entry to the cell, this protein is subjected to high selective pressure. In this study, the locations of mutations in the structures of mutant HA were analyzed and the three-dimensional (3D) structures of these mutations were modeled in I-TASSER. Also, the location of these mutations was visualized and studied using Swiss PDB Viewer software and the PyMOL Molecular Graphics System. The crystal structure of the HA from A/California/07/2009 (3LZG) was used for further analysis. The new noncovalent bond formations in mutant luciferases were analyzed via WHAT IF and PIC, and protein stability was evaluated in the iStable server. We identified 33 and 23 mutations in A/Shiraz/106/2015 and A/California/07/2009 isolates, respectively; some mutations are located on the antigenic sites of Sa, Sb, Ca1, Ca2, and Cb HA1 and the fusion peptide of HA2. The results show that with the mutation some interactions are lost and new interactions are formed with other amino acids. The results of the free-energy analysis suggested that these new interactions have a destabilizing effect, which needs confirmation experimentally. IMPORTANCE Due to the fact that the mutations that occurred in the influenza virus HA cause the instability of the protein produced by the virus and antigenic changes and the escape of the virus from the immune system, the mutations that occurred in A/Shiraz/1/2013 were investigated in terms of energy level and stability. The mutations located in a globular portion of the HA are S188T, Q191H, S270P, K285Q, and P299L. On the other hand, the E374K, E46K-B, S124N-B, and I321V mutations are located in the stem portion of the HA (HA2). The change V252L mutation eliminates interactions with Ala181, Phe147, Leu151, and Trp153 and forms new interactions with Gly195, Asn264, Phe161, Met244, Tyr246, Leu165, and Trp167 which can change the stability of the HA structure. The K166Q mutation, which is located within the antigenic site Sa, causes the virus to escape from the immune response

Prevalence of underlying diseases in died cases of COVID-19: A systematic review and meta-analysis.

IntroductionUnderlying disease have a critical role in vulnerability of populations for a greater morbidity and mortality when they suffer from COVID-19. The aim of current study is evaluating the prevalence of underlying disease in died people with COVID-19.MethodsThe current study have been conducted according to PRISMA guideline. International database including PubMed, Scopus, Web of Science, Cochrane and google scholar were searched for relevant studies up to 1 June. All relevant articles that reported underlying disease in died cases of COVID-19 were included in the analysis.ResultsAfter screening and excluding duplicated and irrelevant studies, 32 articles included in the analysis. The most prevalent comorbidities were hypertension, diabetes, cardiovascular disease, liver disease, lung disease, malignancy, cerebrovascular disease, COPD and asthma. Among all reported underlying disease, highest and lowest prevalence was related to hypertension and asthma which were estimated 46% (37% - 55%) and 3% (2%- 6%), respectively.ConclusionIn summary, underlying disease have a critical role in poor outcomes, severity of disease and high mortality rate of COVID-19 cases. Patients with hypertension, cardiovascular disease and diabetes should be carefully monitored and be aware of health protocols

Prevalence of human metapnemovirus in children with acute respiratory tract infection Shiraz, Iran during 2014-2015

Background: Human metapneumovirus (HMPV) is a newly discovered viral agent of respiratory infections. In present study we determined prevalence of HMPV in children less than10 years with acute respiratory infections (ARTI) that referred to the health centers of Shiraz University of Medical Sciences, Iran.Methods: Nasal swabs were obtained from 180 children less than 10 years old with respiratory tract symptoms during fall, winter and spring seasons of 2014 and 2015. The specimens were tested for HMPV F gene using one step RT-PCR.Results: HMPV was detected in 30 (16.66%) of 180 children with (ARTI) less than 10 years old. Approximately 63.33% of HMPV positive patients aged less than 3 years and 86.33% were younger than 5 years old. The clinical symptoms were bronchiolitis, wheezing and cough.Conclusions: The frequency distribution of HMPV revealed that most patients aged between 1 to 5 years and this virus is one of the respiratory viral agents to causes ATRI, especially children less than 5 years old

A challenging case of carbapenem resistant Klebsiella pneumoniae-related pyogenic liver abscess with capsular polysaccharide hyperproduction: a case report

Abstract Background Carbapenem-resistant Klebsiella pneumoniae (CRKP) infections are a major public health problem, necessitating the administration of polymyxin E (colistin) as a last-line antibiotic. Meanwhile, the mortality rate associated with colistin-resistant K. pneumoniae infections is seriously increasing. On the other hand, importance of administration of carbapenems in promoting colistin resistance in K. pneumoniae is unknown. Case presentation We report a case of K. pneumoniae-related pyogenic liver abscess in which susceptible K. pneumoniae transformed into carbapenem- and colistin-resistant K. pneumoniae during treatment with imipenem. The case of pyogenic liver abscess was a 50-year-old man with diabetes and liver transplant who was admitted to Abu Ali Sina Hospital in Shiraz. The K. pneumoniae isolate responsible for community-acquired pyogenic liver abscess was isolated and identified. The K. pneumoniae isolate was sensitive to all tested antibiotics except ampicillin in the antimicrobial susceptibility test and was identified as a non-K1/K2 classical K. pneumoniae (cKp) strain. Multilocus sequence typing (MLST) identified the isolate as sequence type 54 (ST54). Based on the patient’s request, he was discharged to continue treatment at another center. After two months, he was readmitted due to fever and progressive constitutional symptoms. During treatment with imipenem, the strain acquired bla OXA−48 and showed resistance to carbapenems and was identified as a multidrug resistant (MDR) strain. The minimum inhibitory concentration (MIC) test for colistin was performed by broth microdilution method and the strain was sensitive to colistin (MIC < 2 µg/mL). Meanwhile, on blood agar, the colonies had a sticky consistency and adhered to the culture medium (sticky mucoviscous colonies). Quantitative real-time PCR and biofilm formation assay revealed that the CRKP strain increased capsule wzi gene expression and produced slime in response to imipenem. Finally, K. pneumoniae-related pyogenic liver abscess with resistance to a wide range of antibiotics, including the last-line antibiotics colistin and tigecycline, led to sepsis and death. Conclusions Based on this information, can we have a theoretical hypothesis that imipenem is a promoter of resistance to carbapenems and colistin in K. pneumoniae? This needs more attention

Cross Sectional Study of Burn Infections and Antibiotic Susceptibility Pattern for the Improvement of Treatment Policy

Introduction: Burn is a devastating form of trauma, and based on its condition, it could run the risk of infections. Infection of wound is a major cause of morbidity and mortality in burn cases. The current study investigates the prevalence of infectious agent in three years and antibiotic resistant pattern to improve and predispose a good policy of treatment in our environment. Materials and Methods: In the present study, a total number of 3330 samples from 713 patients were evaluated for detection of the most prevalent infections and for finding out the antibiotic susceptibility pattern with routine microbiology procedures. Results: Based on the results, 598 samples were reported positive. According to the results Pseudomonas aeruginosa, Coagulase Negative Staphylococcus and Acinetobacter sp. were the three most prevalent bacteria with a prevalence rate of 42.1%, 22.1% and 18.4% respectively. Furthermore, based on the results of distribution and diversity of bacterial infections, wound samples were the most infected samples with 73.6% of total infections. Finally, during these three years, there were no significant changes in the resistance pattern of Gram positive and Gram negative infectious agents. Conclusion: By evaluating the infectious agents during the period of the study, it was found that due to the focus on treatment of Gram negative bacteria, Gram positive bacteria especially Staphylococcus aureus and Coagulase Negative Staphylococcus have at least doubled. This increase in two important nosocomial infections is a next threat of infection and septicemia for burn victims