Jundishapur Journal of Microbiology
Volume:9 Issue: 9, Sep 2016

Research to understand and control the emergence and spread of antimicrobial resistance has become a public health priority.
This study was conducted to study epidemiology and resistant pattern of bacteria causing infection in different King Khalid hospital units.
Patients and All samples were sent to the lab and routinely processed according to the standard microbiological procedures. Then, the cultures yielding growth were selected for the study. Identification and antibiotic susceptibility test for all clinical isolates were processed by using MicroScan instrumentation. A total of 428 clinical samples were collected within 8 months; out of them, 300 clinical isolates were subjected to validation test.
Escherichia coli, Klebsiella pneumonia, and Pseudomonas aeruginosa were the commonly identified Gram-negative bacteria. Staphylococcus aureus was the only identified Gram-positive bacterium. The most common infections were taken from the wounds (39.0%), urinary tract (32.3%), and bloodstream (17.8%). The most common antibiotic-resistant bacteria were found on female surgical ward (100%) followed by ICU (90.2%), and male surgical ward (88.2%). The overall results of antibiotic resistance were 100% for S. aureus, 93.3% K. pneumonia, 75.7 % E. coli, and 100% for P. aeruginosa. Staphylococcus aureus showed high resistance to ampicillin and linezolid (94.1%). High (86.95%) and full resistance (100%) against ampicillin were observed from E. coli and K. pneumonia, respectively. P. aeruginosa was fully resistant to 4 antibiotics of cefazoline, cefoxitin, tetracycline, and trimethoprim-sulfamethoxazole.
The study was useful in determining the risk factors and defining different hospital units which should be targeted for measures to prevent infection.

Helicobacter pylori is a major human pathogenic bacterium in gastric mucosa. Although the association between gastric cancer and H. pylori has been well-established, the molecular mechanisms underlying H. pylori-induced carcinogenesis are still under investigation. MicroRNAs (miRNAs) are small noncoding RNAs that modulate gene expression at the posttranscriptional level. Recently, studies have revealed that miRNAs are involved in immune response and host cell response to bacteria. Also, microRNA-375 (miR-375) is a key regulator of epithelial properties that are necessary for securing epithelium-immune system cross-talk. It has been recently reported that miR-375 acts as an inhibitor of H. pylori-induced gastric carcinogenesis. There are few reports on miRNA-mediated targeting long noncoding RNAs (lncRNAs).
This study aimed to examine the possible effect of miR-375 as an inhibitor of H. pylori-induced carcinogenesis on the expression of lncRNA SOX2 overlapping transcript (SOX2OT) and SOX2, a master regulator of pluripotency of cancer stem cells.
In a model cell line, NT-2 was transfected with the constructed expression vector pEGFP-C1 contained miR-375. The RNA isolations and cDNA synthesis were performed after 48 hours of transformation. Expression of miR-375 and SOX2OT and SOX2 were quantified using real-time polymerase chain reaction and compared with control cells transfected with pEGFP-C1-Mock clone. Cell cycle modification was also compared after transfections using the flow cytometry analysis.
Following ectopic expression of miR-375, SOX2OT and SOX2 expression analysis revealed a significant decrease in their expression level (P This is the first report to show down-regulation of SOX2OT and SOX2 following induced expression of miR-375. This finding may suggest expression regulation potential between different classes of ncRNAs, for example between miR-375 and SOX2OT. This data not only extends our understanding of possible ncRNA interactions in cancers but also may open novel investigation lines towards elucidation of molecular mechanisms controlling H. pylori inflammation and carcinogenesis.

Bacterial resistance to antibiotics has become a major source of concern for public health. Pseudomonas aeruginosa strains are important opportunistic pathogens. These bacteria have a high resistance to a wide range of existing antimicrobials and antibiotics.
The present study was performed to evaluate the frequency of KPC in P. aeruginosa isolated from clinical samples of educational hospitals of Arak University of Medical Sciences, using the mentioned phenotypic and genotypic methods.
One hundred and eight non-duplicate clinical isolates of P. aeruginosa were collected from hospitals of Arak University of Medical Sciences, Arak, Iran. Antibacterial susceptibility was determined by the disk diffusion method. KPC production was confirmed by the Modified Hodge Test (MHT), which is a phenotypic test, and combined-disk test with boronic acid and the Polymerase Chain Reaction (PCR).
In the present study, 13 isolates (12%) of P. aeruginosa were positive for KPC, using PCR. Comparison of the two phenotypic methods used in this study showed that boronic acid is more sensitive than MHT in identification of KPC-producing strains (84.6% vs. 77%).
Utilization of reliable methods for identifying carbapenemase-producing strains and determining their antibiotic resistance pattern could have a very important role in treatment of infections caused by these strains. A substantial amount of P. aeruginosa isolated from clinical samples of hospitals in Arak (Iran) produce KPC carbapenemase. Due to their low specificity, MHT and boronic acid phenotypic methods could not completely identify KPC-producing P. aeruginosa. However, the sensitivity of boronic acid phenotypic method in detection of KPC was higher than MHT.

The success of endodontic treatment depends on a few crucial factors. One of these factors is the complete chemomechanic preparation of root canal against various bacteria. In particular, the effect of resistant bacteria may cause intense pain with flare-up and formation of periapical lesions. Therefore, the strong effect of irrigants plays an important role in terms of the complete elimination of these bacteria to achieve long-term successful treatment.
The aim of this study was to investigate the antibacterial effects of super-oxidized water (SPO) in root canals infected with Enterococcus faecalis biofilms.
One hundred twenty single-root, premolar teeth were selected. Initially, the teeth were prepared and then disinfected. E. faecalis were inoculated and kept at 37°C for 24 hours in the root canals. The re-inoculation procedure was repeated on the first, fourth, seventh, and tenth days. The infected root canals were divided into one negative (saline) and one positive (sodium hypochlorite) control group and four experimental groups (super-oxidized water: 1, 2, 3, or 5 minutes) (n = 20). Paper points were placed in the root canals to control and evaluate the biofilm formation. Biofilms were counted on blood agar plates, and data was evaluated and statistically analyzed using one-way ANOVA and Tukey’s test.
Although sodium hypochlorite (NaOCl) showed no statistically significant difference when compared with three and five minutes of SPO irrigation (P > 0.05), NaOCl showed statistically significant differences among all other groups (P Super-oxidized water indicated a remarkable and similar bactericidal effect to that of traditional NaOCl against E. faecalis biofilms. In terms of successful endodontic treatment approaches, super-oxidized water may be used as an effective irrigation solution in clinics.

The highest incidence of listeriosis, due to consumption of ready-to-eat foods and fresh, shredded, minimally processed vegetables, occurs among pregnant women and the elderly. In order to reduce the prevalence of listeriosis among consumers, better protective measures are recommended. Chitosan films, with or without added essential oils, represent a modern, safe method of preserving the quality of such vegetables and significantly reducing the incidence of Listeria monocytogenes in these foods.
The present study was conducted to evaluate the antimicrobial properties of composite chitosan-gelatin films with and without essential oils against two strains of L. monocytogenes, ATCC 19115 and ATCC 19112, in fresh shredded cabbage.
Shredded cabbage was inoculated with L. monocytogenes and packed between two layers of the chitosan composite film, then placed in Petri dishes. The prepared samples were stored at 4°C then analyzed for total viable count on PALCAM agar while incubated at 37°C, every 24 hours for 7 days.
Average L. monocytogenes content ranged from 4.2 - 5.4 log CFU/g, reaching values of 7.2 - 8.6 log CFU/g in samples of untreated cabbage. A complete reduction of L. monocytogenes ATCC 19115 on cabbage was achieved after 120 hours in the presence of 0.5% chitosan film, whereas reduction of L. monocytogenes ATCC 19112 was achieved after 144 hours. In the presence of 1% chitosan film, the bacteria withered more quickly and complete reduction of both species of L. monocytogenes was achieved after 96 hours.
All tested formulations of chitosan films exhibited strong antimicrobial activity on the growth of both strains of L. monocytogenes on cabbage. The best effect was achieved with a 1% chitosan concentration. The addition of essential oils increased the antimicrobial activity of all tested films.

Toxoplasmosis is a life-threatening infection in organ transplant recipients, people receiving corticosteroid or radiation therapy, people with malignancies, and AIDS patients.
The current study aimed to determine the prevalence of toxoplasmosis in patients receiving chemotherapy for malignancies in the Bushehr province of southwest Iran.
Blood samples were taken from 86 patients who were continuously referred to the chemotherapy center in Bushehr province and evaluated by ELISA to determine anti-Toxoplasma IgG and IgM antibodies. Moreover, a blood buffy coat of each sample was assessed by polymerase chain reaction (PCR), targeting a 529 bp gene of T. gondii. PCR products of the positive samples were sequenced to determine the genotype of the parasite.
Anti-Toxoplasma IgG antibodies were detected in the sera of 21 (24.4%) cases. All of the patients were negative for anti-Toxoplasma IgM antibodies. No statistically significant correlation was found between seropositivity to Toxoplasma and duration of chemotherapy or having contact with cats. PCR detected a 529 bp band of T. gondii in the buffy coats of two out of 86 (2.3%) cases. The sequence analysis demonstrated that both cases were 95% identical to type III (VEG strain) of T. gondii.
Findings of this study demonstrated the presence of type III T. gondii in the buffy coats of patients undergoing chemotherapy. Given that toxoplasmosis is a life-threatening infection in immunocompromised patients, these patients should be screened for toxoplasmosis before and during chemotherapy to prevent acute toxoplasmosis.

Years after the development of antituberculosis (TB) drugs, many people continue to suffer from this disease. To control the spread of TB, strains of the Mycobacterium tuberculosis complex need to be determined, and sources of infection must be identified. Such steps should help to prevent transmission of the infection.
The aim of this study was to perform molecular genotyping of isolates of the M. tuberculosis complex obtained from patients in northwestern Iran.
One hundred ninety-four culture-positive M. tuberculosis isolates obtained from patients in northwestern Iran were analyzed using the mycobacterial interspersed repetitive unit-exact tandem repeats (MIRU-ETR) method.
The MIRU-ETR method distinguished 162 different patterns in the 194 isolates, comprising 23 clusters and 139 unique patterns. Its discriminatory power according to the Hunter-Gaston discriminatory index (HGDI) was 0.9978. The largest cluster contained six isolates.
This research indicated that various strains of M. tuberculosis were responsible for TB and that the majority of cases were due to reactivation.

Microemulsions (MEs), which consist of oil, water, surfactants, and cosurfactants, have recently generated considerable interest as antimicrobial agents.
To determine the antifungal and antiviral activities of three ME formulations (MEa, MEb, and MEc) that differ in their hydrophilicity.
The ME formulas were produced by mixing different fractions of Tween 80, Span 20, ethanol, oil, isopropyl myristate, and distilled water. The antifungal activity of the ME formulas against Aspergillus niger, A. flavus, Bacillus, Candida albicans, and C. glabrata were determined by the solid medium diffusion cytotoxicity test against the mitochondria, measuring the minimum inhibitory concentration, dry biomass, and leakage of potassium, and characterizing the cell morphology. The antiviral activities of the ME formulas against the herpes simplex virus type 2 (HSV-2) were determined using the cytopathic effect assay.
Significant antimicrobial activities were recorded against A. niger and herpes simplex virus type 2 (HSV-2) when treated with MEb that had hydrophobic nanodroplets with an average diameter of 4.7 ± 1.22 nm. A volume of 0.1 mL of MEb (10 mL of potato dextrose broth) inhibited the germination of A. niger cells, reduced their dry biomass, enhanced the leakage of potassium from the cell membranes, affected their mitochondria, and altered the shape of their conidia, in addition to enlarging them. MEb was able to destroy the HSV-2 virus at a 200-fold dilution in Dulbecco’s modified eagle medium.
The water-in-oil ME with equivalent surfactant-to-oil ratio (MEb) has great potential as an antifungal and antiviral agent.

A major characteristic of Candida biofilm cells that differentiates them from free-floating cells is their high tolerance to antifungal drugs. This high resistance is attributed to particular biofilm properties, including the accumulation of extrapolymeric substances, morphogenetic switching, and metabolic flexibility.
This study evaluated the roles of metabolic processes (in particular the glyoxylate cycle) on biofilm formation, antifungal drug resistance, morphology, and cell wall components.
Growth, adhesion, biofilm formation, and cell wall carbohydrate composition were quantified for isogenic Candida albicans ICL1/ICL1, ICL1/icl1, and icl1/icl1 strains. The morphology and topography of these strains were compared by light microscopy and scanning electron microscopy. FKS1 (glucan synthase), ERG11 (14-α-demethylase), and CDR2 (efflux pump) mRNA levels were quantified using qRT-PCR.
The ICL1/icl1 and icl1/icl1 strains formed similar biofilms and exhibited analogous drug-tolerance levels to the control ICL1/ICL1 strains. Furthermore, the drug sequestration ability of β-1, 3-glucan, a major carbohydrate component of the extracellular matrix, was not impaired. However, the inactivation of ICL1 did impair morphogenesis. ICL1 deletion also had a considerable effect on the expression of the FKS1, ERG11, and CDR2 genes. FKS1 and ERG11 were upregulated in ICL1/icl1 and icl1/icl1 cells throughout the biofilm developmental stages, and CDR2 was upregulated at the early phase. However, their expression was downregulated compared to the control ICL1/ICL1 strain.
We conclude that the glyoxylate cycle is not a specific determinant of biofilm drug resistance.

Acute respiratory tract infection (ARTI) is one of the most common infections worldwide, causing significant morbidity and mortality.
This study was conducted to determine the prevalence and seasonal distribution of respiratory viruses in our region, in children and adults with a pre-diagnosis of ARTI.
A total of 845 nasopharyngeal swab specimens were analyzed with the RespiFinder Smart 22 kit (PathoFinder BV, Netherlands) and the Rotor-Gene 6000 real-time PCR system.
At least one pathogen was detected in 612 (72.4%) of the specimens. Overall, 902 pathogens were detected; 821 (91%) were viruses and 81 (9%) were bacteria. The most commonly detected pathogens were influenza A virus (IFV-A) (n = 219), influenza B virus (IFV-B) (n=157), rhinovirus/enterovirus (n = 107), human bocavirus (HBoV) (n = 91), respiratory syncytial virus (RSV) A/B (n = 64), adenovirus (n = 56), human coronaviruses (n = 51), Mycoplasma pneumoniae (n = 49), parainfluenza viruses (n = 40), human metapneumovirus (n = 36), Bordetella pertussis (n = 15), Legionella pneumophila (n = 11), and Chlamydophila pneumoniae (n = 6), respectively. Among the 215 (25.4%) co-infected cases, IFV-A/HBoV and IFV-A/IFV-B were the most common co-infections. IFV-A was the most prevalent agent in all age groups except for children under 5 years of age, in whom RSV A/B was the most common pathogen. Approximately two thirds of the respiratory viruses were detected in early spring and winter, with peaks in January, March, and April.
With regard to the prevalence and seasonal distribution of respiratory viruses, our epidemiological data for the 2014 - 2015 season in Istanbul showed a predominance of IFV-A infections with a peak activity in early spring. Enhanced surveillance and early detection of respiratory viral pathogens can be useful in the diagnosis, treatment, and prevention of ARTIs, and for guiding the development of appropriate public health strategies.

Bacteria utilize various methods in order to live in protection from adverse environmental conditions. One such method involves biofilm formation; however, this formation is dependent on many factors. The type and concentration of substances such as sugars that are present in an environment can be effective facilitators of biofilm formation.
First, the physico-chemical properties of the bacteria and the target surface were studied via the MATS and contact angle measurement methods. Additionally, adhesion to different surfaces in the presence of various concentrations of sugars was compared in order to evaluate the effect of these factors on the biofilm formation of Escherichia coli, which represents a major food contaminant.
Results showed that the presence of sugars has no effect on the bacterial growth rate; all three concentrations of sugars were hydrophilic and demonstrated a high affinity toward binding to the surfaces.
The impact of sugars and other factors on biofilm formation can vary depending on the type of bacteria present.