Avicenna Journal of Clinical Microbiology and Infection
Year:2019 | Volume:6 | Issue:1|Papers Count:7

Dear Editor, In April 2003, the Human Genome Project (HGP) was completed after 13 years of continuous genome analysis using Sanger sequencing (1). More than 20 institutions, companies, and laboratories were involved in HGP. Although this is commonly acknowledged as a historical improvement in human genetic studies, there are still hundreds of genomic gaps left which must be resolved. Furthermore, the project costed nearly $3 billion (roughly $5 billion considering inflation)! Nowadays, however, such enterprise can be finished only in one day, at a cost a little more than a grant per sample, thanks to next generation sequencing (NGS) platforms. NGS (e. g. Roche, Illumina, SOLiD) and the further novel technology of next-next generation sequencing (e. g. Pac-Bio SMRT) have obviously fueled genetic studies, especially molecular cancer studies, at dramatically lower costs (2)...

Background: The uropathogenic Escherichia coli (UPEC) is an important bacterium that colonizes the bladder mucous membrane as biofilm and causes urinary tract infection (UTI). In addition, UPEC favors long-term persistence and leads to relapses in untreatable UTI. Further, bacterial hydrophobic interactions play a role in bacterial adherence to the surface and facilitate biofilm formation due to adhesion. Similarly, cell surface hydrophobicity (CSH), fimbriae, curli fiber, and colanic capsule allow UPEC isolates to initiate infections. Considering the above-mentioned explanation, this study evaluated the association between genes encoding curli fimbriae, colanic acid (CA) capsule, and f1c fimbriae with biofilm formation and CSH among UPEC isolates. Methods: To this end, 100 Escherichia coli strains were isolated from the urine samples of the patients and were diagnosed by biochemical tests. Furthermore, a tissue culture plate method was used to determine the capacity of biofilm formation, followed by conducting microbial adhesion to hydrocarbons method for CSH determination. Finally, the presence of csgA, csgD, rcsA, rcsC, and foc genes was determined by applying polymerase chain reaction. Results: Totally, 40, 22, and 28 isolates had strong, moderate, and weak biofilm formation capacity, respectively. Moreover, 42 and 38 isolates had strong and moderate CSH. Similarly, among the isolates with strong CSH, 32, 13, and 5 isolates had strong, moderate and weak biofilm formation capacity and the prevalence of csgA, csgD, rcsA, and foc genes was 33, 35, 35, 16, and 29, respectively. Based on the findings, no significant difference was observed between the frequency of csgA, csgD, rcsA, rcsC, and foc genes among the strong, moderate, and weak biofilm producers. Conclusions: In general, there is an association between CSH and the biofilm formation of UPEC isolates. This result showed the role of CSH as an effective factor on bacterial adhesion for the first stage of biofilm formation. However, differentiating the strains is not confirmed regarding their ability to form biofilms and their CSH and the presence of all studied genes.

Background: Pseudomonas aeruginosa as a gram-negative bacterium can be detected all around us, as it is generally distributed in different environments and can act as a probable cause of human diseases especially in immunocompromised patients. This bacterium also is a leading cause of nosocomial infections in burn intensive care units. The aim of this study was to evaluate the presence of some virulence genes in P. aeruginosa isolated from different sources. Methods: Pseudomonas aeruginosa isolates were evaluated for the presence of virulence factors including toxA, phzM, lasB, exoU, exoS genes by polymerase chain reaction (PCR). Results: According to our findings, the prevalence of toxA, phzM, lasB, exoU, and exoS virulence genes in the isolates originated from human sources was 86%, 16%, 94%, 100%, and 78%, respectively. While, the above-mentioned virulence factors were present in 46%, 4%, 68%, 64%, and 62% of environmental samples, respectively. Conclusions: Findings of this study indicated that the presence of virulence genes in human isolates was greater than their presence in environmental isolates. Hence, it seems this difference may have caused infections in humans.

Background: LL-37 is one of the well-known antimicrobial peptides which is effective on the extended expecetrome of microbial pathogens. The aim of this study was to design a modified digital analog of LL-37 with enhanced antimicrobial activity and restricted toxicity of the host cell. Methods: Online databases and software were used for determining LL-37 characteristics such as hydrophobicity, Booman index, and hemolysis probability. Variant structures based on the replacement of leucine and lysine with tryptophan and arginine were calculated as well. Finally, the best sequence was selected and analyzed for approving as an antimicrobial peptide. Results: The antibacterial characteristics of LL-37 were improved by replacing the arginine and tryptophan and according to systemic calculations, it was defined that this peptide is an antimicrobial peptide by 97% confidential. Conclusions: In general, bioinformatics tools are considered as one of the most available and efficient tools for antimicrobial peptide designing. Therefore, future studies could use kLL-39 as an antimicrobial peptide and investigate its antimicrobial effects in vitro.

Background: Capnocytophaga canimorsus and C. cynodegmi, as gram-negative rods, are commensal in the oral cavities of dogs and cats and C. canimorsus can occasionally cause fatal systemic infections in humans. In addition, most human infections, caused by C. canimorsus, are associated with dog bites, licking pre-existing wounds, or the other contact with dogs. Therefore, the aim of this study was to evaluate the role of polymerase chain reaction (PCR) in detecting C. canimorsus and C. cynodegmi in oral swab samples of dogs and cats. Methods: To this end, oral swabs were taken from 125 dogs and 35 cats enriched in the anaerobic atmosphere and then were used for DNA isolation and evaluated by PCR. Results: In 125 dog oral swabs, DNA of Capnocytophaga genus was prespecified in 32% of these samples (n=40). Further, 20 and 36 samples were positive for DNA of C. canimorsus and C. cynodegmi, respectively, when PCR was performed for the DNA of Capnocytophaga spp. Similarly, 23 out of 35 oral swabs of the cats were positive for the presence of the DNA of Capnocytophaga genus. Finally, all the samples were positive for the DNA of C. cynodegmi when they were analyzed by the primer specified Capnocytophaga species while only 15 samples were positive for the presence of DNA of C. canimorsus. Conclusions: Overall, the risk of infection with C. canimorsus is high because of the presence of the bacteria in the mouth of cats and dogs and severe consequences of infection for humans. Therefore, the owners of cats and dogs should be informed about this risk, especially if the owners belong to specific risk groups like young children, pregnant women, elderly people, and immunocompromised patients.

Background: This study aimed to determine the chemical composition of Origanum syriacum L., as well as to assess the antimicrobial activity of O. syriacum essential oil and its constituents. Methods: To this end, O. syriacum plants were collected from their native growing locations in western and coastal governorates of Syria. Next, the composition of the essential oil from every station was determined by gas chromatography (GC) and then by high-performance liquid chromatography (HPLC) to estimate the number and the quantity of all components. Preparative-HPLC was used to isolate the essential oil components. Then, the identified constituents of the essential oils were confirmed utilizing GC-mass spectrometry. Microdilution broth susceptibility assay was applied and the first well without turbidity was considered as the minimum inhibitory concentration. Results: The results showed that ß-myrcene (21. 93%), carvacrol (19. 20%), anisaldehyde (7. 57%), thymol (7. 40%), γ – terpinene (5. 27%), and sabinene (4. 43%) were the main components of bulk essential oils. Similarly, only minor qualitative and quantitative variation was found between locations. The antibacterial activity of bulk essential oil and its components was evaluated against gram-negative local isolates of Escherichia coli O157, Salmonella enterica, Klebsiella pneumoniae, Yersinia enterocolitica O9, Brucella melitensis, Proteus mirabilis, and Pseudomonas aeruginosa. Although the bulk essential oil inhibits all the bacteria except for E. coli O157 at the highest tested concentration (48 μ L/mL), the essential oil components differ in their antibacterial activity. Conclusions: Overall, thymol and carvacrol represented the most antibacterial activity compared to the other substances.

In this review, the studies in which potential correlation between the area under the curve/minimum inhibitory concentration ratio of vancomycin (AUC/MIC) and its efficacy and safety had been considered, were assessed. Papers that had defined the potential correlation between vancomycin AUC/MIC and its efficacy, safety, or both as a primary outcome were included. Considering that extent of vancomycin exposure as well as susceptibility of microorganisms were both included, AUC/MIC seemed to be a more accurate index than serum trough concentration for predicting vancomycin efficacy. However, data regarding correlation between this index and vancomycin-induced nephrotoxicity are limited. Different breakpoints have been defined for AUC/MIC. The optimized use of vancomycin can improve its efficacy and defer the occurrence of tolerance. Further studies are needed to define optimum vancomycin AUC/MIC breakpoints and in turn predict its efficacy and safety.