نشریه میکروب شناسی پزشکی ایران
سال دهم شماره 6 (بهمن و اسفند 1395)

Urinary tract infection (UTI) is one of the most common infections, and Escherichia coli is so far the most common causative agent of this disease. The O antigen, consisting of many repeats of an oligosaccharide unit, is part of the lipopolysaccharide (LPS) in the outer membrane of Gram-negative bacteria. The variability of the O antigen provides the major basis for serological schemes of Gram-negative bacteria. The aim of this study was to investigate the prevalence of O-serogroups among E. coli isolated from patients with UTI.
During three months, 210 patients with urinary tract infection, referred to three hospitals of Tehran, Sanandaj and Boroujerd. E. coli isolates were identified using standard methods then serogrouping was performed by using PCR method.
A total of 150 E. coli strains were isolated from the urine samples. The most common types of O antigens were O1 (13.33%), O16 (8%), O8 (5.33%) and O21 (4%). There was no positive isolate for O22 and O83 genes.
The present study revealed that serogroup O1 was isolated with maximum frequency followed by O16, O8 and O21, respectively. In UPEC, the O-serogroups can be related to the virulence factor profile of each strain. Further studies from other parts of Iran and on other serogroup are recommended.

With increase Staphylococcus epidermidis infections, discrimination between invasive and non-invasive S. epidermidis strains and determination of drug resistance, for diagnosis and treatment is important.
From August 2014 to March 2015, 123 strains isolated from patients and medical instruments from Ali Asghar and Hazrat Rasoul hospitals were used to discriminate invasive and contaminating S. epidermidis strains by ica, atlE, agrA, sarA, and mecA genes by Multiplex PCR method. Also, according to the CLSI standards, resistance to cefoxitin, linzeolid, clindamycin, erythromycin and tetracycline were tested by disk diffusion method and vancomycin E-test method.
prevalence of ica and mecA genes were 85% and 75% in invasive strains and 20% and 51% in contaminating strains, respectively. The resistance level to cefoxitin, tetracycline, clindamycin and erythromycin antibiotics in invasive strains were: 75℅, 35℅, 37℅, 76℅ and in contaminating strains were; 51℅, 40℅, 30℅, 64℅, respectively. Resistance to vancomycin and linezolid was not observed in this study.
This study shown that ica gene can be used as a suitable marker for discrimination between invasive and contaminating isolates. Also, vancomycin is a better choice for the treatment of resistant patients to methicillin.

E.coli is a gram-negative bacillus from the family of Enterobacteriaceae. E. coli bacteria is used as a water indicator of urban sewage pollution. The repeating sequences, are replications of the genes or parts of them that are repeated. Tandem repeats may be available for the number of iterations in a different creature than other populations, which are called as consequent replications with variable numbers. The purpose of this study was to evaluate the diversity of repeated sequences of ms06 and ms23 loci in E. coli strains isolated from water resources in Alborz province.
A total of 72 E.coli isolates which obtained from water sources in Alborz, Iran, from September 2012 to October in 2013, were analyzed, then standard and biochemical tests were used to identify and isolate E. coli bacteria, after that, DNA extraction was performed by boiling method. The diversity of repeated sequences of ms06 and ms23 loci in E. coli was conducted using polymerase chain reaction.
The current study showed that the locus ms06 had five different alleles (1 repeat, 2 repeat, 3 repeat, 4 repeat, 5 repeat) and locus ms23 showed four alleles (1 repeat, 2 repeat, 2.5 repeat). It is also founded that ms23 loci contain a null allele.
This is the first study on the diversity of repeated sequences in E.coli strains isolated from water resources in Alborz. In this study, the variation of repeated sequences was high.

Surface bacterial contamination has been shown to be a potential source of cross-infection. The aim of this study was to identify resistant bacterial isolates in the dental clinic before and after disinfection and evaluation of biofilm formation by them.
Sampling was performed at a dental clinic in Isfahan, Iran, on 2014. Samples were obtained by using swab and settle plate method. In the firs method, sterile swabs were used to sample of dental instrument and unit chair surface before and after disinfection, then swabs were transferred to TSB media (60 tubes). In the second method, air monitoring was carried out by settling blood agar and nutrient agar plates at the certain distance from the patient for 1 hour (24 plates). Then these samples incubated aerobically for 2 days at 37°C. Isolates were identified to species level with morphological and biochemical features and 16S ribosomal RNA gene sequencing. In addition, the strength of biofilm formation by isolates was measured by using microtiter plate method.
Most of these isolates were spore-forming Bacillus species and environmental Staphylococcus species. On the basis of the strength of biofilm formation, the most important identified bacteria were Staphylococcus xylosus and Bacillus safensis.
Bacteria that are able to form biofilm, can survive after disinfection of dental instruments and can enhance the risk of infection in dental practice by providing a surface for colonization of pathogens.

Nowadays, prebiotics are the matter of interest, because of stimulating the growth and activity of beneficial enteric bacteria (probiotic) and their antimicrobial and antitumor characteristics. The aim of this research is to study the effect of prebiotic Chitosan on the growth of probiotic bacteria and their antimicrobial effect.
This research was done in 2010 in order to study of the effect of prebiotic chitosan on the growth of probiotic bacteria Lactobacillus acidophilus PTCC 1643 and Lactobacillus casei PTCC 1608 by using of drawing growth curve of these bacteria in the presence of different chitosan concentrations, also, the effect of this prebiotic on antimicrobial properties of probiotic bacteria was investigated against Escherichia coli by using of overlay method and blank disk method.
According to the test results, the growth of two probiotic bacteria were increased in the presence of chitosan and the most effective concentration of prebiotic chitosan was achieved, 6.5 (mg/mL).Antimicrobial effects of probiotic bacteria were increased in the presence of chitosan against E.coli especially Entrohaemoragic E. coli in comparison with the time that probiotic bacteria were used alone.
According to the results of this study, prebiotic chitosan, due to increasing effect on the growth and antimicrobial characteristic of probiotic lactobacillus, can be a proper candidate for effective symbiotic compound against pathogenic bacteria.

Using active antimicrobial packaging reduce the risks of growth of pathogenic or spoilage microorganisms in foods. In this study, antimicrobial activity of poly lactic acid (PLA) films containing different concentrations (0, 0.5, 1 and 1.5%) of Trachyspermum ammi essential oil and ethanolic extract of propolis (0, 1 and 2%) was evaluated against Listeria monocytogenes, Staphylococcus aureus, Escherichia coli O157:H7 and vibrio parahaemolyticus by using disk diffusion assay.
Circular discs of poly lactic acid films incorporated by essential oil and ethanolic extract of propolis, prepared by casting method on glass petri dishes, were placed on Muller-Hinton agar plates that previously inoculated by tested bacteria. Diameters of inhibition zones were measured after 24 h incubation of plates at 35o C, by using Digital Caliper and Digimizer software.
Result of this study showed that the inhibition zone was increased with increasing concentration of essential oil for all tested bacteria. Also, gram positive bacteria were more sensitive to the poly lactic acid films containing essential oil than gram negative bacteria. The results revealed that L. monocytogenes was the most sensitive bacteria against films containing Trachyspermum ammi essential oil alone or in combination by ethanolic extract of propolis. Also, poly lactic acid films containing ethanolic extract of propolis showed no inhibitory effects against all tested bacteria.
Poly lactic acid films containing Trachyspermum ammi essential oil have a high potential for antimicrobial food packaging applications to enhance the safety of food products.

The mortality of the Rotavirus diarrhea still remains a major problem among developing countries. The aim of this study was to evaluate the prevalence of rotavirus among children below 5 years with acute diarrhea who admitted in reference one of Hospitals (Hospital Abuzar) is located in Ahvaz.
The study was conducted as a cross-sectional survey on 200 fecal samples taken from children under 5 years of age with gastroenteritis, referred to Abuzar hospital in Ahwaz. Sampling started in January 2014 and continued until September 2014. Samples were transported to the laboratory in the Department of Virology, Ahvaz Jundishapur University of Medical Science and were tested. The latex agglutination test was performed on samples and the RT-PCR was tested for accurate detection of rotavirus. Data was analyzed using SPSS software.
Of the 200 samples collected, latex agglutination test and RT-PCR confirmed the presence of rotavirus in 41% and 21% of cases, respectively. Positive samples were equally in boys and girls. The highest incidence was observed in children under 2 years of age (88.1%) and in the age range of 6-8 months (28.57%). Diarrhea, vomiting and fever were the most common symptom of the disease and powdered milk consumption was observed in 50% of the positive samples. Also, the highest and the lowest number of positive samples were reported in February-March 2014 and August- September 2014, respectively.
According to the high percentage of Rotavirus infection in different region of Iran, continuous monitoring of the amount of Rotavirus gastroenteritis is recommended in healthcare centres.

Enterococci are normal flora and present in the intestinal tract of humans and many mammals. Today, the increasing prevalence of resistant enterococci to aminoglycosides is a major problem in hospitals around the world. In Enterococci, aph (3 ') - IIIa gene plays a major role in the emergence of resistance to streptomycin. The aim of this study was to identify this gene in enterococci isolated from patients using PCR method in Tehran.
In this study, 350 clinical samples were collected from Milad, Imam Khomeini, and Baghiyatallah hospitals during the years 2015-2014. Enterococcus species were identified based on specific biochemical tests and culture. Then, disk diffusion method was performed according to CLSI guidelines to determine the drug resistance of Enterococcus isolates to different antibiotics. The following primer to streptomycin resistance genes, aph (3 ') - IIIa was used in the PCR method.
Among the 150 samples, 87 samples (58%) were reported as Enterococcus faecalis, and 63 (42%) as Enterococcus faecium. In Antibiotic test, strains showed high resistance to tetracycline and erythromycin whereas the least resistance was observed to chloramphenicol and vancomycin, respectively. The high resistance to Streptomycin was in 22.2% strains which included aph (3') -IIIa gene.
The results of this study can be concluded that the presence of aph (3') -IIIa gene is the main cause of antibiotic resistance to streptomycin in Enterococcus faecium and E. faecalis strains that is growing gradually in the hospitals in Tehran. Therefore, early detection of this type of resistance with the PCR method could be the best way to prevent the spread of infections caused by this bacterium.

Antibiotic resistance has prompted the use of medicinal plants with fewer side effects instead of common drugs. The aim of this study was to determine the antibiotic resistance pattern in coagulase-positive Staphylococcus aureus isolated from ready to eat foods in Kashan, 2015.
In this cross-sectional study in 2015, 384 samples (including 60 salad, 40 frozen vegetable, 120 traditional ice cream, 90 sweet, 40 hamburger and 34 kebab samples) were randomized purchased of local markets in Kashan and evaluated for the occurrence of S. aureus by culturing methods. The obtained isolates were subjected to disc diffusion antimicrobial susceptibility tests. Also, susceptibility of the obtained isolates were evaluated by disc diffusion to eucalyptus, lavender, lemon, tarragon, basil and cumin essential oils.
Results and Out of 384 samples, 4 (1.042%) samples were contaminated with coagulase-positive S. aureus. The two isolates (50%) were sensitive to co-trimoxazole. Out of the 4 isolates, 100% were found to be resistant to methicillin, penicillin, oxacillin, cefoxitin, kanamycin, vancomycin, tetracycline, ciprofloxacin, chloramphenicol, amoxicillin, ampicillin, cefotaxime, nitrofurantoin, norfloxacin, ceftriaxone and gentamicin. None of the isolates were resistant in D test. Also, the highest inhibitory effect on growth of S. aureus related to cumin, eucalyptus, lavender essential oils. The obtained results showed the high antibiotic resistance of S. aureus isolated from ready to eat foods. In addition, noted essential oils with anti-S. aureus effects can be used in the preparation of antibacterial drugs.

One of the major problems for the isolation and detection of S. pneumoniae from clinical specimens, high sensitivity, rapid autolysis and thus the inability to hold isolates of pneumococcus. So, it is essential to use specific techniques for the preservation of the organism. In this study several different cultures for S. pneumoniae isolates were compared and evaluated.
In 2014, 2 ATCC standard , 30 clinical, and 30 normal flora pneumococcal available isolates were selected from a previous study. Dorset egg medium was prepared for midterm preservation, three storage environments, including Skim milk-Tryptone-Glucose-Glycerin (STGG), nutrient broth enriched and Todd Hewitt Broth (THB) was constructed to long-term preservation, and their performance on maintenance pneumococcal isolates was assessed.
Results and 95% of the isolates cultured on Dorset after 70 days and 80% after four months later had the ability to grow. All three long-term storage environment, had a good performance for one year but enriched nutrient broth could keep bacteria with but better-quality up to 2 years. There is no difference between isolates from the patients and isolates from normal flora to survive in the environment. Also aggressive origin of iclinical isolates had no effect on their survival rate. Dorset egg (DE) medium can be considered as a simple, low cost and efficient, medium for midterm preservation and enriched nutrient broth for long term storage of pneumococcal isolates in clinical laboratories.

Due to immune deficiency diseases (cancer, transplant recipients and HIV) environmental mycobacteria infections are increasing. Forasmuch as the clinical symptons of environmental mycobacteria lung infections and tuberculosis are similar, due to difference of diet therapy between environmental mycobacterium infections and Mycobacterium tuberculosis, it is necessary to identify and differentiate Mycobacterium species. Molecular methods seem to be a useful tool for detection and differentiation of Mycobacterium species.