Jundishapur Journal of Microbiology
Volume:9 Issue: 5, May 2016

Group A β-hemolytic Streptococcus is the most common cause of bacterial pharyngitis among 5 - 15-year-old children, but it is uncommon in children less than three years old and rarely happens in infants less than one year old.
The patient was a 62-day-old female infant who presented with fever and poor feeding since two days before admission. At the time of admission, the patient was febrile and ill. Upon examination, a rectal temperature of 38.5°C, multiple right-sided submandibular lymphadenopathies, pharyngeal erythema, and tonsillar exudates were detected. Twenty-four hours after the throat swab was collected and cultured, Streptococcus pyogenes grew on a sheep blood agar medium. The patient’s mother, who also experienced similar symptoms, had a positive throat swab culture for S. pyogenes.
Although Streptococcal pharyngitis is rare in children less than three years old and the necessity of treatment is not well clarified, in case of streptococcal infection in parents and the occurrence of similar signs and symptoms in their child, considering S. pharyngitis as a possible differential diagnosis seems rational.

It has been revealed that Staphylococcus aureus enterotoxin B (SEB) may feature anti-cancer and anti-metastatic advantages due to its ability to modify cell immunity processes and signaling pathways. Glioblastoma is one of the most aggressive human cancers; it has a high mortality nature, which makes it an attractive area for the development of novel therapies.
We examined whether the SEB could exert its growth inhibitory effects on glioblastoma cells partially through the manipulation of a key tumor growth factor termed transforming growth factor-beta (TGF-β).
A human primary glioblastoma cell line, U87, was treated with different concentrations of SEB. The cell quantity was measured by the MTT assay at different exposure times. For molecular assessments, total ribonucleic acid (RNA) was extracted from either non-treated or SEB-treated cells. Subsequently, the gene expression of TGF-β transducers, smad2/3, at the messenger RNA (mRNA) level, was analyzed via a quantitative real-time polymerase chain reaction (qPCR) using the SYBR Green method. Significant differences between cell viability and gene expression levels were determined (Prism 5.0 software) using a one-way analysis of variance (ANOVA) test.
We reported that SEB could effectively down-regulate smad2/3 expression in glioblastoma cells at concentrations as quantity as 1 μg/mL and 2 μg/mL (P We suggested that SEB could represent an agent that can significantly decrease smad2/3 expression in glioblastoma cells, leading to moderate TGF-β growth signaling and the reduction of tumor cell proliferation.

Helicobacter pylori cause chronic gastritis and subsequent diseases like gastric and duodenal ulcers and gastric adenocarcinoma. Current methods for detecting H. pylori have several disadvantages and it is of utmost importance to develop a simple, quick, accurate, and cost-effective diagnostic test.
The aim of this study was to set up and evaluate a diagnostic value of loop- mediated isothermal amplification (LAMP) for detecting H. pylori.
Patients and The analytical sensitivity values (limit of detection) of LAMP and polymerase chain reaction (PCR) were determined using serial dilutions of H. pylori DNA. Analytical specificity of the methods using new designed primers targeted ureC gene was also determined.
The detection limits of the LAMP and PCR assay were similar and were 10 fg of pure DNA of H. pylori, which is equal to 6 copy numbers of H. pylori genome. Analytical specificity of the tests was 100% because the tests were positive only with H. pylori DNA.
The analytical sensitivity of LAMP and PCR methods, using the designed primers, was 8 times more than any other reported methods. The designed methods are specific and sensitive for detection of H. pylori in different clinical and environmental samples.

Drug design against human immunodeficiency virus type 1 (HIV-1) integrase through its mechanistic study is of great interest in the area in biological research. The main obstacle in this area is the absence of the full-length crystal structure for HIV-1 integrase to be used as a model. A complete structure, similar to HIV-1 of a prototype foamy virus integrase in complex with DNA, including all conservative residues, is available and has been extensively used in recent investigations.
The aim of this study was to determine whether the above model is precisely representative of HIV-1 integrase. This would critically determine the success of any designed drug using the model in deactivation of integrase and AIDS treatment.
Primarily, a new structure for HIV-1 was constructed, using a crystal structure of prototype foamy virus as the starting structure. The constructed structure of HIV-1 integrase was simultaneously simulated with a prototype foamy virus integrase on a separate occasion.
Our results indicate that the HIV-1 system behaves differently from the prototype foamy virus in terms of folding, hydration, hydrophobicity of binding site and stability.
Based on our findings, we can conclude that HIV-1 integrase is vastly different from the prototype foamy virus integrase and does not resemble it, and the modeling output of the prototype foamy virus simulations could not be simply generalized to HIV-1 integrase. Therefore, our HIV-1 model seems to be more representative and more useful for future research.

Helicobacter pylori is an important pathogen of human gastric mucosa. Antibiotic resistance, especially resistance to clarithromycin is a major factor for treatment failure of H. pylori infections. The main mechanism of clarithromycin resistance in these bacteria is related to point mutations in three different locations of 23S rRNA gene.
The aims of this study were to evaluate the resistance rate to clarithromycin among local H. pylori isolates by the E-test method and to determine the profile of point mutation in 23S rRNA by real-time polymerase chain reaction (PCR) method.
Patients and Eighty biopsy samples were collected from dyspeptic patients by endoscopy during 2011 - 2012. All samples were homogenized immediately and cultured on supplemented brucella blood agar and incubated under microaerophilic conditions. Further biochemical tests and ureC gene PCR was done for H. pylori confirmation. The H. pylori OC1096 strain was used as the control strain, simultaneously. Frequency of clarithromycin resistance was determined by the E-test method based on the clinical and laboratory standard institute (CLSI) standards. Point mutation profile was determined by real-time PCR and further analysis of melting curve, amplicon sequencing was done continuously.
From 80 biopsy samples, 20 positive H. pylori isolates were detected and confirmed by biochemical tests and PCR method. Overall, 21.7% of the H. pylori isolates, showed clarithromycin resistance phenotype by use of the E-test. Also, the minimal inhibitory concentration of clarithromycin was determined as ≥ 0.5 mg/L by the E-test method. Only point mutation in the location of A2143G with melting temperature of 54.7°C was observed in all resistant isolates.
This study showed that the frequency of H. pylori clarithromycin resistance in Iran is relatively high. Since clarithromycin is not commonly used in Iran for H. pylori eradication, the high rate of resistance could be related to cross-reactivity between other macrolides. Therefore, macrolide antibiotics must be prescribed with precaution in any case of treatment other than H. pylori infections. All resistant isolates showed A2143G mutation in 23S rRNA as the dominant pattern of point mutation at least in Tehran H. pylori isolates.

Haemophilus influenzae type b (Hib) infection has high morbidity and mortality rate, especially in children under 5 years of age. Enzyme-linked immunosorbent assay (ELISA) technique is the most used method to detect antibodies against H. influenzae. Available commercial ELISA kits are expensive and not always readily available, particularly for epidemiological studies.
This study was performed to develop and optimize a homemade ELISA kit for the detection of Hib anti-polyribosylribitol phosphate (PRP) antibodies in children.
To develop and optimize an indirect ELISA method, pure PRP was prepared. The PRP was coupled to bovine serum albumin, using sodium periodate. Then optimal conditions for ELISA, including coating antigen concentration and peroxidase labeled conjugate concentrations, incubation temperature and incubation time, were determined. To confirm the efficacy of optimized kit, 83 serum samples from non-vaccinated children, aged less than 6 years were collected and analyzed, using homemade and commercial ELISA.
The optimal conditions were considered to perform ELISA. Comparison between results obtained from optimized ELISA kit and commercial ELISA kit showed a good agreement.
Taking into account these data, we elaborated a homemade ELISA kit that is an efficacious and cost-effective substitute for commercial kit, in disease control and diagnosis.

Carbapenem resistant Acinetobacter baumannii is an important nosocomial pathogen associated with a variety of infections.
The current study aimed to characterize the antimicrobial susceptibility, analyze the prevalence of oxacillinase and metallo-β-lactamase (MBL) genes and molecular typing of clinical isolates of A. baumannii.
A total of 124 non-repetitive isolates of A. baumannii were collected from various clinical specimens in two teaching hospitals in Ahvaz, south-west of Iran. Antimicrobial susceptibility test was carried out by disk diffusion method. The minimum inhibitory concentrations (MICs) of imipenem, meropenem, colistin and tigecycline were determined using E-test. To screen for MBL production, double disk synergy (DDs) test and MBL E-test were performed. The presence of blaOXA-23-like, blaOXA-24-like, blaOXA-51-like, blaOXA-58-like, blaVIM, blaIMP and blaSPM genes was assessed by polymerase chain reaction (PCR). To identify clonal relatedness, all isolates were subjected to repetitive sequence-based PCR (rep-PCR).
Based on disk diffusion results, the highest rate of resistance was observed in rifampin (96.8%). Colistin and polymyxin-B were the most effective agents in vitro. According to the MIC results, the rate of resistance to imipenem, meropenem, colistin and tigecycline were 78.2%, 73.4%, 0.8% and 0, respectively. Metallo-β-lactamase production was positive in 42.3% and 79.4% of the isolates by DDs test and E-test, respectively. All isolates (100%) carried blaOXA-51-like gene. According to the results of multiplex PCR, blaOXA-23-like and blaOXA-24-like genes were detected in 85.6% and 6.2% of carbapenem resistant isolates, respectively. No blaOXA-58- like, blaVIM, blaIMP and blaSPM were detected. By rep-PCR, carbapenem resistant isolates were separated into six genotypes (A to F). Genotype A (30.9%) was the most prevalent (P value The rate of carbapenem resistant A. baumannii isolates were high in this study. Since, blaOXA-58-like or MBL genes were not detected, it seems that resistance to carbapenems is related to blaOXA-23-like and blaOXA-24-like. Moreover, blaOXA-23-like was the most prevalent oxacillinase (OXA) gene. Most of the isolates belonged to one of the four dominant genotypes indicating clonal dissemination in the hospitals under study. In order to control the spread of carbapenem-resistant A. baumannii, infection- control strategies are needed.

Intracellular aspartic proteinase A enzyme is expressed by the APR1 gene and is one of the important factors in the development of systemic candidiasis caused by Candida albicans.
The aim of this study was to evaluate the expression of the APR1 gene in C. albicans isolates obtained from patients with multiple sclerosis (MS) and from controls.
Patients and The samples were obtained from 135 MS patients with candidiasis and 100 matched controls of healthy individuals during 2010 - 2011. The clinical and control isolates of C. albicans obtained from individuals were cultured onto sabouraud dextrose agar (SDA). The evaluation of APR1 gene expression was performed using the reverse transcriptase-polymerase chain reaction (RT-PCR) method.
There was a statistically significant difference in APR1 gene expression of C. albicans strains between MS patients (mean ± SD: 0.5208 ± 0.11518) and the control group (mean ± SD: 0.7603 ± 0.11405) (P = 0.000). Significant correlations were found between the APR1 gene expression of C. albicans strains from MS patients with regard to age and the expanded disability status scale (EDSS) (P = 0.000). The mean values of EDSS were 1.6074 ± 0.1081 after antifungal treatment and 2.2519 ± 0.1323 before antifungal treatment (P = 0.000). No significant correlation was observed between the APR1 gene expression with regard to sex and MS subtypes.
The results suggested that APR1 gene expression in C. albicans strains isolated from MS patients may be an important factor for invasive C. albicans strains in the progression of MS disease.

Human cytomegalovirus (HCMV) infections are a major cause of morbidity and mortality among immunocompromised patients. Prolonged antiviral therapy is a cause of mutation and drug resistance in the HCMV genome.
The aim of this study was to identify resistance to ganciclovir (GCV) in Iranian immunosuppressed patients at two different stages of the disease: early (before GCV is initiated) and late (after six months of GCV therapy).
Patients and In this study, 87 specimens from Iranian patients were amplified using nested PCR amplification of the UL97 gene. Sequence analyses of products were performed for identifying the mutated codons.
The present study show that the most frequent GCV-resistant mutations occurred in codons A594V (26.43%), H520Q (18.39%), and M460V (13.79%), consequently occurring at a low frequency in the L595S (2.29%), E596G (1.14%), and Del 594 (1.14%) codons, and with intermediate frequency in the C592G (10.34%), M460I (9.19%), and C603W (6.89%) codons. We describe for the first time a new GCV-resistance mutation, the deletion of codon 594, in the UL97 gene of Iranian HCMV patients after GCV therapy, following renal transplantation.
The findings of the present study can be utilized to detect GCV resistance patterns among Iranian immunocompromised patients and to treat HCMV infections accordingly.

Candida glabrata is a pathogenic yeast with several unique biological features and associated with an increased incidence rate of candidiasis. It exhibits a great degree of variation in its pathogenicity and antifungal susceptibility.
The aim of the present study was to evaluate the in vitro antifungal susceptibilities of the following six antifungal drugs against clinical C. glabrata strains: amphotericin B (AmB), ketoconazole (KTZ), fluconazole (FCZ), itraconazole (ITZ), voriconazole (VCZ), and caspofungin (CASP).
Forty clinical C. glabrata strains were investigated using DNA sequencing. The in vitro antifungal susceptibility was determined as described in clinical laboratory standard institute (CLSI) documents (M27-A3 and M27-S4).
The sequence analysis of the isolate confirmed as C. glabrata and deposited on NCBI GenBank under the accession number no. KT763084-KT763123. The geometric mean MICs against all the tested strains were as follows, in increasing order: CASP (0.17 g/mL), VCZ (0.67 g/mL), AmB (1.1 g/mL), ITZ (1.82 g/mL), KTZ (1.85 g/mL), and FCZ (6.7 g/mL). The resistance rates of the isolates to CASP, FCZ, ITZ, VZ, KTZ, and AmB were 5%, 10%, 72.5%, 37.5%, 47.5%, and 27.5%, respectively.
These findings confirm that CASP, compared to the other antifungals, is the potent agent for treating candidiasis caused by C. glabrata. However, the clinical efficacy of these novel antifungals remains to be determined.

Excessive consumption of antimicrobial materials in hospitals is considered as the main encoder leading to the emergence, development and acquisition of new bacterial resistance to beta-lactamase.
Owing to the lack of proper information regarding the mechanism of the bacterial resistance to antibiotics and responsible genes in the country, the current study aimed to consider the resistance or sensitivity of the Acinetobacter baumannii multi drug resistant (MDR) isolates facing 2% glutaraldehyde. The study was conducted in the selected intensive care units in Tehran hospitals, Iran, in 2013.
In this study conducted over a period of 10 months, A. baumannii species were isolated by bacterial culture following biochemical tests from intensive care units (ICUs) of some hospitals in Tehran, Iran (Fayazbaksh, Taleghani, Imam Khomeini, Valiasr, Labafinejad). The resistance and sensitivity of the isolates to antibiotics were considered according to the clinical and laboratory standard institute CLSI (2012) guidelines. By multiplex PCR method, blaCTX and blaTEM genes were detected and finally, MDR strains were treated with 2% glutaraldehyde. PCR was used for each strain of MDR using specific primers.
In the current study, 131 A. baumannii isolates (22.3%) out of 588 were studied. The level of resistance to various antibiotics was in the range of 69.4% to 100%. The frequencies of blaTEM and blaCTX genes were 3.2% and 19.4%, respectively. MIC50% and MIC90% of imipenem and meropenem antibiotics were 32 ± 1 µg/mL and 64 ± 1 µg/mL, respectively (P It seems that besides the variety and prevalence of blaTEM and blaCTX, enormous mechanisms such as porin and leaking systems (efflux pumps) are responsible for the information of the A. baumannii resistance to disinfectants. The study on an accurate consideration of the resistance in strains and other microorganisms is advised.

The highest incidence of meningitis occurs during the neonatal period and (then) infancy. Although Bacterial agents are the most dangerous cause of neonatal and childhood meningitis yet viruses especially, enteroviruses (EV), are by far the most common cause of meningitis in this age group.
The aim of the current study was to evaluate the role of EVs in neonatal and childhood meningitis in the Mashhad city of Iran.
This was a descriptive study that was performed at Imam Reza hospital in a period of six months (March to September 2007), during which all of the cerebral spinal fluid (CSF) samples from the neonatal intensive care unit (NICU) and pediatrics ward were collected and real time-polymerase chain reaction (RT-PCR) for EVs was done on these samples. Clinical data were collected retrospectively from hospital files.
We collected 58 CSF samples (35 neonates and 23 children) during six months. Pleocytosis of CSF was seen in 51.1% of the subjects (28% of neonates, and 66.6% of infants and children). Enteroviruses PCR was positive in 37.1% (13) of neonates and 34.7% (8) of children. Pleocytosis of CSF was seen in 23% and 75% of EV positive neonates and children, respectively. Polymorphonuclear (PMN) dominance (PMN > 50%) of CSF was seen in 50% and 33% of EV positive neonates and children, respectively. There were three cases of bacterial meningitis in our group; EV PCR result was positive for one of these subjects. Concomitant bacterial infection (meningitis and sepsis) was seen in 9.5% (two cases) of EV positive CSFs in our study. Almost half of the available neonates (four of nine) with pure enteroviral meningitis (EVM) were discharged (in good condition) with final diagnosis of culture negative sepsis (CNS) and mean length of hospital stay (MLOS) of 4.3 days. One (12.5%) of the neonates with EVM, who had a very low birth weight ( Enteroviruses were a common cause (> 30%) of meningitis in our study group. Concomitant bacterial infection is not rare in neonates and children with EVM. Many of the neonates (50%) and almost all of the children with EVM did not require prolonged hospitalization. Both normal CSF and PMN dominancy of CSF was common in neonates and children with EVM. Positive qualitative CRP of serum (up to two plus) was common especially in children with EVM. Non-symptomatic mild hyponatremia/SIADH was common in early life EVM.

Pili in Streptococcus pneumoniae have been shown to be one of the adherence factors for epithelial cells in the human upper respiratory tract. Two types of pilus-like structures (pilus islet-1 and pilus islet-2) have been distinguished in S. pneumoniae.
To investigate the presence of pilus islet-1 (PI-1) in S. pneumoniae and the correlation between our isolates.
In this study, 162 S. pneumoniae isolates were collected from clinical specimens, and normal flora were also examined for the distribution of PI-1 using the presence of the rlrA and rrgC genes as markers for this islet and sipA as an indicator of pilus islet-2 (PI-2). BOX-PCR analyses were performed to determine the genetic relationship between isolates.
The results confirmed the presence of rlrA and rrgC genes in both clinical (n = 39) and normal flora (n = 26) isolates. The minimal inhibitory concentration results revealed that the rate of resistance of these isolates to the three antibiotics tested ranged from 26% for penicillin to 46% for erythromycin and tetracycline. Furthermore, 12% of the isolates were resistant to all three antibiotics. Strain typing using repetitive element BOX-PCR analysis among the 65 isolates identified 8 different band patterns.
Our results indicated that the dissemination of PI-1 was widespread in S. pneumoniae isolates, although no PI-2 isolates were detected. Furthermore, the frequency of rlrA and rrgC of clinical isolates was significantly more than that of normal flora isolates.

Crimean-Congo hemorrhagic fever (CCHF) is an arboviral zoonotic disease transmitted to humans mainly through the bite of blood-sucking Ixodidae ticks and also via contact with the blood and tissues of infected livestock.
This study is a retrospective descriptive survey based on data collected from the health center of Khuzestan province, Iran, during 1999 - 2015.
Patients and Patients with symptoms of severe headache, high fever, and bleeding were evaluated. Laboratory tests and serological or molecular assays were used to detect probable and confirmed cases, respectively. The epidemiological parameters of this study were analyzed on the basis of probable cases.
A total of 42 patients were diagnosed as probable cases, and 17 of these (42.5%) were confirmed serologically. Two peaks of the disease occurred in Khuzestan province, in 2003 and 2010, with seven cases each of those years, leading to the deaths of five and two patients, respectively. Men and women comprised 57.1% and 42.9% of the patients, respectively. Of all probable cases, 64.3% were from urban areas and 35.7% were from rural areas. The age groups of 10 - 19 and 20 - 29 years, with a frequency of 26.2% in each group, were exposed to the most infections. Farmers and housewives were the highest at-risk occupational groups with a frequency of 28.6% and 26%, respectively. Fever, bleeding, and thrombocytopenia were reported in 95% of the patients, and the case-fatality ratio was calculated to be 28.6% (12 of 42 cases).
Continuous training is necessary to improve the knowledge and awareness of the highest-risk groups with regard to the transmission modes, prevention, symptoms, and treatment of this disease.