Alterations in the gut microbiota and their metabolites in human intestinal epithelial cells of patients with colorectal cancer

BACKGROUND

The gut microbiota has become one of the main risk factors for the formation and development of colorectal cancer (CRC). CRC intensification may be due to the microbial pathogens' colonization and their released metabolites. Here, we analyzed Bacteroidetes and Clostridia bacteria in CRC patients and studied bacterial metabolome in cancerous tissues compared to their adjacent normal tissues.

METHODS AND RESULTS

The population of selected bacteria in biopsy specimens of 30 patients with CRC was studied by RT-qPCR. The mutagenicity and cytotoxicity effects of microbiota metabolites were evaluated by Ames test and MTT Assay, respectively. Moreover, gene expression in carcinogenic pathways was studied by RT-qPCR, and genes with different expressions in tumor and non-tumor tissues were diagnosed. Based on microbiota analysis, the relative abundance of Clostridia and C. difficile was significantly higher in CRC tissue, whereas C. perfringens showed higher relative abundance in normal tissue. AIMES test confirmed the proliferation and mutagenicity effects of the bacterial metabolites in CRC patients. Significant upregulation of C-Myc, GRB2, IL-8, EGFR, PI3K, and AKT and downregulation of ATM were observed in CRC samples compared to the control.

CONCLUSIONS

The influence of bacterial metabolites on inflammation and altered expression of genes in the cell signaling pathways was observed. The findings confirm the role gut microbiota composition and bacterial metabolites as key players in CRC onset and development.

Epstein-barr virus/Helicobacter pylori coinfection and gastric cancer: the possible role of viral gene expression and shp1 methylation

Background and Objectives

Among the various factors involved in the development of gastric cancer (GC), infectious agents are one of the most important causative inducers. This study aimed to investigate the possible role of EBV gene expression on SHP1 methylation in co-infection with Helicobacter pylori in patients with GC.

Materials and Methods

Formalin-fixed paraffin-embedded samples were obtained from 150 patients with gastrointestinal disorders. The presence of the H. pylori and EBV genome were examined by PCR. The expression level of viral gene transcripts and methylation status of the SHP1 cellular gene was assessed by quantitative real-time PCR and methyl-specific PCR.

Results

EBV and H. pylori coinfection were reported in 5.6% of patients. The mean DNA viral load was significant in patients coinfected with cagA-positive H. pylori (P= 0.02). The expression of BZLF1 and EBER was associated with GC. Also, the expression level of BZLF1in GC tissues was significantly higher in coinfection (P = 0.01). SHP1 methylation frequency was higher in the GC group than in the control group (P = 0.04). The correlation between the methylation rate and the H. pylori infection was highly significant (P<0.0001). The strongest positive correlation was observed in GC specimens between SHP1 methylation and H. pylori cagA-positive strains (p= 0.003).

Conclusion

Our results suggested that cagA might involve in the elevation of EBV lytic gene expression and SHP1 methylation, and the development of gastric cancer. Understanding the mechanism of EBV H. pylori - cagA + coinfection, as well as host epigenetic changes, can play an important role in diagnosing and preventing gastric cancer.

Viral aetiology of acute central nervous system infections in children, Iran

Introduction. Viral infections are increasingly an important cause of central nervous system (CNS) complications.

Hypothesis/Gap Statement. There is no comprehensive insight about CNS infections due to viral agents among Iranian children.

Aim. This study aimed to investigate the viral aetiology, clinical and epidemiological profile of children with acute infections of the CNS.

Methodology. A prospective study was conducted on children at the referral hospital in Isfahan, Iran, from June 2019 to June 2020. A multiplex PCR assay was used to detect the viral causative agent in cerebrospinal fluid and throat/rectal swab samples.

Results. Among 103 patients with eligible criteria, a confirmed or probable viral aetiology was detected in 41 (39.8 %) patients, including enteroviruses – 56.1 %, herpes simplex virus 1/2 (HSV-1/2) – 31.7 %, Epstein-Barr virus – 17.1 %, varicella-zoster virus (VZV) – 9.7 %, influenza A virus (H1N1) –4.9 % and mumps – 2.4 %. There was a higher proportion of PCR-positive samples in infants than in other age groups. Encephalitis and meningoencephalitis were diagnosed in 68.3 % (28/41) and 22 % (9/41) PCR-positive cases, respectively.

Conclusion. The findings of this research provide insights into the clinical and viral aetiological patterns of acute CNS infections in Iran, and the importance of molecular methods to identify CNS viruses. HSV and VZV were identified as important causes of encephalitis in young children.

A Phage Cocktail To Control Surface Colonization by Proteus mirabilis in Catheter-Associated Urinary Tract Infections

Proteus mirabilis is a biofilm-forming bacterium and one of the most common causes of catheter-associated urinary tract infections (CAUTIs). The rapid spread of multidrug-resistant P. mirabilis represents a severe threat to management of nosocomial infections. This study aimed to isolate a potent phage cocktail and assess its potential to control urinary tract infections caused by biofilm-forming P. mirabilis. Two lytic phages, Isf-Pm1 and Isf-Pm2, were isolated and characterized by proteome analysis, transmission electron microscopy, and whole-genome sequencing. The host range and effect of the phage cocktail to reduce the biofilm formation were assessed by a cell adhesion assay in Vero cells and a phantom bladder model. The samples treated with the phage cocktail showed a significant reduction (65%) in the biofilm mass. Anti-quorum sensing and quantitative real-time PCR assays were also used to assess the amounts of transcription of genes involved in quorum sensing and biofilm formation. Furthermore, the phage-treated samples showed a downregulation of genes involved in the biofilm formation. In conclusion, these results highlight the efficacy of two isolated phages to control the biofilms produced by P. mirabilis CAUTIs. IMPORTANCE The rapid spread of multidrug-resistant (MDR) and extensively drug-resistant (XDR) bacterial strains and biofilm formation of bacteria have severely restricted the use of antibiotics and become a challenging issue in hospitals. Therefore, there is a necessity for alternative or complementary treatment measures, such as the use of virulent bacteriophages (phages), as effective therapeutic strategies.

Genetic Diversity of Helicobacter pylori Isolates from Patients with Gastric Diseases in Isfahan

Background

Helicobacter pylori (H. pylori), a spiral-shaped bacterium colonizing the human stomach, is generally acquired in childhood. This pathogen is highly diverse and can be used as genetic markers for predict the history of human migrations. This study aimed to determine the genetic diversity of H. pylori isolates from patients with dyspepsia by the multi-locus sequence typing (MLST) and update data on the prevalence of H. pylori among Iranian dyspeptic patients.

Materials and Methods

In this descriptive cross-sectional study, 165 gastric biopsy specimens were obtained from patients with dyspepsia referred to Dr. Shariati Hospital of Isfahan, Iran, from April to July 2018. The status of H. pylori infection was determined by FISH in paraffin-embedded biopsy specimens. MLST of seven housekeeping genes was performed for 20 H. pylori isolates. The phylogenetic tree was plotted using CLC v8 and iTol software.

Results

The overall prevalence of H. pylori infection was 53.3%. In the results of the analysis of MLST, a total of 14 new STs were recorded. The results of the global analysis showed that all the isolates, with a wide diversity, have a genetic affinity with members of the European population, such as Italy and Russia, and are in the hpEurope haplotype.

Conclusion

Given the high prevalence of H. pylori infection in this region, early and accurate identification of patients seems necessary. Sequence analysis and determination of the origin of the phylogeny of strains can be effective in clinical management and monitoring of risk factors for chronic and recurrence of infection.

The characteristic and potential therapeutic effect of isolated multidrug-resistant Acinetobacter baumannii lytic phage

BACKGROUND

Widespread misuse of antibiotics caused bacterial resistance increasingly become a serious threat. Bacteriophage therapy promises alternative treatment strategies for combatting drug-resistant bacterial infections. In this study, we isolated and characterized a novel, potent lytic bacteriophage against multi-drug resistant (MDR) Acinetobacter baumannii and described the lytic capability and endolysin activity of the phage to evaluate the potential in phage therapy.

METHODS

A novel phage, pIsf-AB02, was isolated from hospital sewage. The morphological analysis, its host range, growth characteristics, stability under various conditions, genomic restriction pattern were systematically investigated. The protein pattern of the phage was analyzed, and the endolysin activity of the phage was determined under the non-denaturing condition on SDS-PAGE. The optimal lytic titer of phage was assessed by co-culture of the phage with clinical MDR A. baumannii isolates. Finally, HeLa cells were used to examine the safety of the phage.

RESULTS

The morphological analysis revealed that the pIsf-AB02 phage displays morphology resembling the Myoviridae family. It can quickly destroy 56.3% (27/48) of clinical MDR A. baumannii isolates. This virulent phage could decrease the bacterial host cells (from 10⁸ CFU/ml to 10³ CFU/ml) in 30 min. The optimum stability of the phage was observed at 37 °C. pH 7 is the most suitable condition to maintain phage stability. The 15 kDa protein encoded by pIsf-AB02 was detected to have endolysin activity. pIsf-AB02 did not show cytotoxicity to HeLa cells, and it can save HeLa cells from A. baumannii infection.

CONCLUSION

In this study, we isolated a novel lytic MDR A. baumannii bacteriophage, pIsf-AB02. This phage showed suitable stability at different temperatures and pHs, and demonstrated potent in vitro endolysin activity. pIsf-AB02 may be a good candidate as a therapeutic agent to control nosocomial infections caused by MDR A. baumannii.

Determination of Capsular Serotypes, Antibiotic Susceptibility Pattern, and Molecular Mechanism of Erythromycin Resistance among Clinical Isolates of Group B Streptococcus in Isfahan, Iran

Background:

Documented streptococcal resistance to erythromycin has recently been raised. The aim of this study is to identify the molecular mechanism of erythromycin resistance among group B Streptococcus (GBS) strains and to correlate with the clinical origin of strains.

Materials and Methods:

A total number of 134 colonizing (n = 36), invasive (n = 36), noninvasive (n = 46), and asymptomatic (n = 16) GBS isolates were characterized by the detection of dltS gene, capsular serotyping, antibiotic susceptibility profiles using disc diffusion method, and screening of the ermB, ermTR, and mefA resistance genes.

Results:

The distribution of capsular serotypes was as follow: serotype III (24.6%), Ia (21.6%), V (17.9%), Ib (14.9%), II (8.9%), IV (8.9%), VI (1.5%), and VII (1.5%). From 134 GBS isolates, 51 (38%) isolates were resistant to erythromycin. The constitutive macrolide lincosamide streptogrmin B (MLSB) was the most common resistance phenotype (62.7%), followed by inducible MLSB (27.4%) and M phenotype (9.8%). Erythromycin resistance rate was higher among asymptomatic GBS strains (13/16, 81.2%). Serotype III was the most prevalent type among resistant isolates (41.1%). The ermB gene highly distributed among resistant strains (64.7%), followed by ermTR (21.5%) and mefA (9.8%). The ermB gene was related to constitutive MLSB phenotype (84.3%, P < 0.05) and serotypes III (61.9%), Ib (87.5%), and V (83.3%). All M phenotype strains harbored mefA gene and were in association with serotype Ia (90%).

Conclusion:

The current study suggests that ribosomal modification with erm genes is the main mechanism of erythromycin resistance. Because of relatively high prevalence of erythromycin resistance, double disc test highly recommended for GBS disease treatment and intrapartum prophylaxis among penicillin intolerant patients in our region.

Significance of the coexistence of non-codon 315 katG, inhA, and oxyR-ahpC intergenic gene mutations among isoniazid-resistant and multidrug-resistant isolates of Mycobacterium tuberculosis: a report of novel mutations

Tuberculosis (TB) is a global threat due to the emergence and spread of drug-resistant Mycobacterium tuberculosis (MTB). Isoniazid (INH) is the main antibiotic used for prevention and treatment of TB. Evidence shows that accumulated mutations can produce INH resistant (INHR) strains, resulting in the progression of multidrug-resistant (MDR) TB. Since point mutations in katG gene, inhA gene, and oxyR-ahpC region correlated with the INH resistance, in this study, we aimed to identify mutations in these three genes in INHR and MDR clinical isolates of MTB by Sanger DNA sequencing analysis. Thirty-three out of 438 isolates were resistant, including 66.7% INHR and 30.3% MDR isolates. In the katG gene, 68.2% INHR isolates had non-synonymous point mutations, mainly R463L (63.6%), and non-synonymous point mutation KatG L587P was seen in one of the MDR isolate. A novel silent substitution L649L was identified in the inhA gene of the MDR isolates. The oxyR-ahpC intergenic region g-88a common mutations (63.6%) in INHR and two distinct novel mutations were found at positions -76 and -77 of the oxyR-ahpC intergenic region. The coexistence of katG non-codon 315 with oxyR-ahpC intergenic region mutations was highly frequent in INHR 59.1% and MDR isolates 70%. Since mutations of all three genes 95.5% lead to the detection of INHR, they might be useful for molecular detection. Our results indicated the continuous evolution and region-specific prevalence of INH resistance. Overall, identification of new mutations in INH resistance can improve the available strategies for diagnosis and control of TB.

Prevalence, population structure, distribution of serotypes, pilus islands and resistance genes among erythromycin-resistant colonizing and invasive Streptococcus agalactiae isolates recovered from pregnant and non-pregnant women in Isfahan, Iran

Background

The information on antibiotic resistance and molecular features of Group B Streptococcus (GBS) are essential for epidemiological purposes as well as vaccine development. Therefore, we aimed to assess the antimicrobial resistance profiles and molecular characteristics of GBS isolates in Isfahan, Iran. A total number of 72 colonizing and invasive GBS were collected from pregnant and non-pregnant women. The GBS isolates were analyzed for resistance profiles, capsular genotyping, and detection of PI-1, PI-2a, PI-2b, hvgA, ermB, ermTR, lnuB and, mefA genes. Besides, erythromycin-resistant strains were subjected to multilocus sequence typing (MLST).

Results

The prevalence of colonizing and invasive GBS were 11 and 0.05%, respectively. The frequency of capsular serotypes was as follows: III (26.3%), Ia (20.83%), Ib and V (each 15.2%), IV (9.7%), II (8.3%), VII (2.7%), and VI (1.3%). Overall frequencies of PIs were as follows: PI-1, 37.5%, PI-1 + PI-2a, 30.5%, PI-1 + PI-2b, 29.1% and PI-2b, 2.7%. Two maternal colonizing GBS (2.6%) were hvgA positive and were belonged to ST-17/CPS-III/PI-1 + PI-2b lineage. Among 30(41.6%) erythromycin resistant GBS, 21 isolates (70%) harbored ermB gene, followed by ermTR (23.3%) and mefA (10%). One clindamycin-resistant isolate harbored the lnuB gene. MLST analysis revealed the following five clonal complexes (CCs) and nine STs: (CC-19/ST-335, ST-19, and ST-197), (CC-12/ST-43, ST-12), (CC-23/ST-163, ST-23), (CC-17/ST-17) and (CC-4/ST-16).

Conclusion

The study shows an alarmingly high prevalence of erythromycin-resistant GBS in Iran. In addition, we report dissemination of ST-335/CPS-III clone associated with tetracycline and erythromycin resistance in our region. The distribution of capsular and pilus genotypes varies between invasive and colonizing GBS that could be helpful for vaccine development.

Cellular miR-101-1 Reduces Efficiently the Replication of HSV-1 in HeLa Cells

INTRODUCTION

Herpes simplex viruses (HSVs) are widely distributed in the human population. HSV type 1 (HSV-1) is responsible for a spectrum of diseases, ranging from gingivostomatitis to keratoconjunctivitis, and encephalitis. The HSVs establish latent infections in nerve cells, and recurrences are common. Their frequent reactivation in elderly and immunosuppressed patients causes serious health complications.

OBJECTIVES

Due to the growing resistance to its main drug, acyclovir, alternative treatments with different mechanisms of action are required. MicroRNAs regulate host and viral gene expression posttranscriptionally. Previous studies reported that mir-101-2 expression has widely participated in the regulation of HSV-1 replication. In this study, we investigate the effect of hsa-miR-101-1 in the replication of HSV-1.

METHODS

We found that transfection of miR-101-1 into HeLa cells could reduce effectively HSV-1 replication using plaque assay and real-time PCR methods.

RESULTS

We showed that overexpression of miR-10-1 produced less viral progeny and manifested a weaker cytopathic effect, without affecting cell viability.

DISCUSSION/CONCLUSION

This result can give us new insights into the control of HSV-1 infections.

SARS-CoV-2, SARS and MERS: Three formidable coronaviruses which have originated from bats

The recent continuously emerging rampancy of novel coronavirus (SARS-CoV-2) that started in Wuhan in late December 2019 has become an international public health emergency and is still spreading rapidly in the world. Up to October 11, 2020, 37.109.6851 confirmed cases of COVID-19 have been announced with 2.8 percent death, which means 1.070.355 confirmed death cases. At the moment, a specific vaccine or drug for the new coronavirus is not available; thus, the development of a drug with far-reaching HCoV inhibitory activity is an urgent medical need. It is, however, vital to first comprehend the nature of this family and other coronaviruses that have caused the outbreak. Here, we relate the epidemiological and virological characteristics of the COVID-19, SARS, and MERS rampancy.

Molecular Characterization of Hospital- and Community-Acquired Streptococcus agalactiae Isolates among Nonpregnant Adults in Isfahan, Iran

Background:

The increasing incidence of Group B Streptococcus (GBS) infection among nonpregnant adults has become of growing clinical and public health concern. The current study investigated the distribution of important virulence determinants and antibiotic susceptibility of GBS isolates causing community acquired (CA) and hospital acquired (HA) infections among nonpregnant adults.

Materials and Methods:

A total of 62 GBS, including 31 CA GBS and 31 HA GBS, were collected from a teaching hospital in Isfahan, Iran. Capsular polysaccharide genotypes (CPS), PI 1, PI 2a, PI 2b, and hypervirulent GBS adhesin (hvgA) virulence genes and antibiotic resistance profiling were determined.

Results:

There were 19 (30.6%) cases of underlying disease that diabetes mellitus (20.9%) was most common. The rate of multidrug resistant GBS strains was accounted for 29%. Distribution of macrolide resistant phenotypes was as follows: constitutive macrolides, lincosamides, and streptogramin B (MLSB) (15 isolates); inducible resistance to MLSB; and L phenotype (each 5 isolates) and M phenotype (1 isolate). V and Ia serotypes were the most predominant capsular type in HA GBS and CA GBS isolates, respectively. The most frequent pilus types were PI 1, PI 1+PI 2a, PI 1+PI 2b, and PI 2a. PI 1 and PI 1+PI 2a had significantly different distributions between CA and HA GBS isolates. Three CA GBS isolates (9.6%) were positive for hvgA gene that belonged to clonal complex 17/sequence type 17/CPS III/PI 1+PI 2b lineage.

Conclusion:

There was a significant difference in the distribution of PIs among CA GBS and HA GBS isolates in our region.

Characterization of Hypervirulent Extended-Spectrum β-Lactamase-Producing Klebsiella pneumoniae Among Urinary Tract Infections: The First Report from Iran

Introduction

This study was conducted to identify the hypermucoviscosity, iron acquisition, and capsule serotypes of K. pneumoniae strains isolated from urinary tract infections among community-acquired patients (CA) and assess the frequency of plasmid-mediated quinolone resistance (PMQR) and extended-spectrum beta-lactamases (ESBL) genes between classic and hypervirulent strains.

Materials and Methods

A total of 105 K. pneumoniae were isolated from CA-UTI. Demographic data related to the underlying diseases and clinical manifestations were further collected. Antibiotic resistance pattern and molecular characterization were compared among ESBL-positive, ESBL-negative, hypervirulent, and classic isolates.

Results

The results revealed that 52.4% of the isolates were confirmed as ESBL producers and 11 (10.5%) were considered as hypervirulent K. pneumoniae (hvKp). Ciprofloxacin and nalidixic acid were the most inactive antibiotics with resistance rates of 68.6% and 64.8%, respectively. Molecular characterization revealed that 7.6% of all the isolates carried k1 and 66.6% carried K2 genes. The most frequent ESBL gene was bla_SHV 63.8%, followed by bla_TEM 59.0%, and bla_CTX-M 58.1%. ESBL genes were significantly more in hvKp than in cKp. Moreover, 61 (84.7%), 47 (65.2%), and 16 (22.2%) of isolates harbored qnrB, qnrS, and qnrA. ESBL genes were detected in all hvKps, and bla_SHV was observed in 90.9% of hvKp (P value= 0.048, 95%).

Discussion

This study reported the high frequency of antimicrobial and multidrug resistance among hvKp isolates. Coexistence of PMQR and ESBL genes in hvkp indicates the necessity to enhance the clinical knowledge and management of hvKp infections.

Efficient process development for high-level production, purification, formulation, and characterization of recombinant mecasermin in Escherichia coli

Overproduction of recombinant mecasermin was achieved by investigation of effect of three factors, temperature, inducer amount, and culture media, at three levels according to the Taguchi statistical design in Escherichia coli in a bench-scale bioreactor. In optimal conditions (induction temperature 28 °C, terrific broth with glucose (TB+G) medium, with 0.1 mM IPTG as inducer) 0.84 g/L mecasermin with expression levels of 38% of total protein and 4.13 g/L final dry cell biomass was produced, that is one of the highest values of recombinant protein has been reported in the batch system. The cell disruption was done by lysozyme pretreatment with sonication to the efficient purification of mecasermin. The isolated and washed inclusion bodies were solubilized in Gdn-HCl at pH 5.4 and folded with glutathione and purified with gel filtration. The purified rhIGF-1 (mecasermin) was formulated with arginine. Mecasermin protein remained t stable at 4 °C for up to 2 years. The quantitative and qualitative control indicated that mecasermin is expressed correctly (without the initial methionine by mass spectrometry), pure (without endotoxin and other protein impurities), correct folding (FTIR, RF-HPLC), monomer form (SEC-HPLC), and active (bioactivity test). Also, the purification results revealed that expression at low temperature results in the efficient purification of the overproduced mecasermin with high quantity and quality.

Determination of surface proteins profile, capsular genotyping, and antibiotic susceptibility patterns of Group B Streptococcus isolated from urinary tract infection of Iranian patients

Objectives

Group B Streptococcus (GBS) is an important opportunistic bacteria that causes a wide range of infections including neonatal sepsis, meningitis, pneumonia, soft tissue and urinary tract infections (UTI). The aim of this study was to evaluate the antimicrobial susceptibility patterns, surface proteins and capsular types of GBS isolates.

Results

100 of UTI isolates were confirmed as GBS. Antimicrobial susceptibility pattern showed that 95% of GBS isolates were resistant to tetracycline, followed by erythromycin (52%), clindamycin (47%), levofloxacin (9%) and penicillin, cefepime, cefotaxime, and ceftriaxone each with (8%), and vancomycin 1%. Common capsular types were III, Ib, V, II, Ia and IV respectively and the distribution of surface protein genes was as follows: rib (40%), alpha-c (22%), alp2/3 (18%) and epsilon (15%), and alp4 gene was not detected in the isolates. Our findings showed the relationship between capsular types with Alpha-like proteins, as well as reduced sensitivity to antibiotics, so the performance of antibiotic surveillance programs is recommended.

Electronic supplementary material

The online version of this article (10.1186/s13104-019-4428-4) contains supplementary material, which is available to authorized users.

Analysis of antibacterial and antibiofilm activity of purified recombinant Azurin from Pseudomonas aeruginosa

Background and Objectives: The aim of this study was to evaluate the antibacterial and antibiofilm activity of recombinant Azurin from Pseudomonas aeruginosa against different bacterial species. Materials and Methods: The azurin gene was cloned in the pET21a vector. The pET21a-azurin construct was transformed into Escherichia coli BL21. The recombinant Azurin was expressed and purified using affinity chromatography and con- firmed by Western blotting. The cytotoxicity of rAzurin was assessed on peripheral blood mononuclear cells. Antibacterial and antibiofilm activity of rAzurin with different concentrations were determined by micro-broth dilution and crystal violet methods, respectively. The effect of rAzurin on bacterial species was statistically analyzed by t- test and spearman correla- tion. Results: The identity of purified protein was confirmed by blotting and distinguished as a 14 kDa band on 15% SDS-PAGE. The IC50 of rAzurin on Peripheral Blood Mononuclear Cell (PBMC) was determined as 377.91±0.5 µg/mL in 24 h. Vibrio cholerae and Campilobacter jejuni displayed the most sensitivity to rAzurin (27.5 and 55 μg/mL, respectively) and the highest resistance (220 μg/mL) was displayed by P. aeruginosa and E. coli. The MIC for other species was 110 μg/mL. The Minimum Biofilm Inhibition Concentration (MBIC) was determined as 220 μg/mL for Salmonella enterica and V. cholerae, 300 μg/mL for Shigella sonnei, Shigella flexneri and P. aeruginosa and 440 μg/mL for the other species. The antimicrobial effect of rAzurin on bacterial species were significant (p value<0.05) and correlation coefficient was negative. Conclusion: The rAzurin appears to be an appropriate choice and a new strategy for prevention of bacterial infection. It inhibits bacterial growth and biofilm formation and candidates as antimicrobial peptides.

Phylogenetic analysis of human bocavirus in children with acute respiratory infections in Iran

Human bocavirus (HBoV) was first characterized in nasopharyngeal aspirates from young children with acute respiratory infections. It is prevalent among children with acute wheezing. This study was carried out in order to analyze the infection frequency and coinfection rates of HBoV with respiratory syncytial virus (RSV) and to perform phylogenetic analysis of HBoV in samples of children with acute respiratory infection in Isfahan, Iran. During the time period 2016-2017, altogether 75 respiratory samples from children hospitalized with acute respiratory infection were collected. The samples were first screened for RSV by direct immunofluorescence method and then subjected to detect HBoV DNA by PCR. Genotyping of HBoV-positive samples was conducted by direct sequencing of PCR products using NP and VP1/VP2 genes. Out of 75 respiratory samples, 20 (26.7%) and 10 (13.3%) were positive for RSV and HBoV, respectively. The coinfection rate was 40% (p = 0.048). Considering the seasonal distribution, winter has the highest extent outbreak (p = 0.036). Sequence analysis of positive samples exhibits that all of the isolated HBoV were related to genotype 1 (HBoV-1) with minimal sequence variations. Increasing frequency of HBoV suggests that the virus is related to acute respiratory infection in children. A single genetic lineage of HBoV1 seems to be the major genotype in Iran.

Inhibition of herpes simplex virus type 1 replication by novel hsa-miR-7704 in vitro

Herpes simplex virus type 1 (HSV-1) infections are one of the most common diseases in human population. HSV-1 causes subclinical, mild to severe diseases, especially in immunocompromised patients. Acyclovir has been used to reduce manifestations of HSV-1 infections. The extensive use of this drug has led to the development of resistant strains. Thus, designing a novel anti-herpes drug with different mechanisms of action is urgently needed. Cellular microRNAs (miRNAs) have direct antiviral effects in addition to their regulatory functions. In this study we used a novel miRNA (hsa-miR-7704), expressed in macrophages, to inhibit HSV-1 lytic infection in HeLa cells. Synthesized hsa-miR-7704 mimics were transfected into HSV-1 infected HeLa cell. The inhibitory effects of the miRNA were evaluated by plaque assay, real time polymerase chain reaction and the viral titers were measured by the 50% tissue culture infective dose (TCID50). The viral titer and cell cytopathic effect were dramatically decreased in HeLa cells transfected with hsa-miR-7704 (50 and 100 nM), compared with HSV-1 infected cells alone or transfected with the mock miRNA control. These results suggest that hsa-miR-7704 inhibits HSV-1 replication efficiently in vitro. This may provide an alternative mechanism to prevent HSV-1 infections.

The rate and importance of Clostridium difficile in colorectal cancer patients

AIM

The aim of this study was to analyze the Clostridium difficile and their toxins in cancerous tissues in comparison to their adjacent healthy tissues in patients with colorectal cancer (CRC) in Iran.

BACKGROUND

Intestinal infection or colonization by microbial pathogens and their released metabolites may have a role in the exacerbation of CRC.

METHODS

A total of 60 biopsy samples from 30 cancerous and 30 adjacent healthy tissues were collected from patients with CRC. Biopsies were homogenized and cultured in cycloserine cefoxitin fructose agar-agar medium to investigate the presence of C. difficile. DNA was extracted, PCR was performed on pure colonies for bacteria detection, and toxin genes were evaluated in each bacterium positive cases. Real-time PCR was performed on extracted DNA for quantitative comparison of Clostridium difficile in healthy and tumor tissues in CRC patients.

RESULTS

Clostridium difficile was isolated from 18 of the cancerous tissue (60%) and 6 of their healthy adjacent tissue (20%) in the culture medium, but toxin genes were positive just in one sample in both groups. Real-time PCR showed the colonization in all samples.

CONCLUSION

This study showed a higher prevalence of Clostridium difficile in cancerous lesions in comparison to healthy tissues. We suggest that the investigation of the rate of CD of colorectal cancer patients before surgery is critical for patients. Further studies with more samples size to study the importance of this bacterium and its toxins in the investigation of colorectal cancer patients survey is recommended.

Antimicrobial Resistance Pattern and Spectrum of Multiple-drug-resistant Enterobacteriaceae in Iranian Hospitalized Patients with Cancer

Background:

Nosocomial infections are one of the most leading causes of morbidity and mortality in patients with cancer. The emergence of multiple-drug-resistant (MDR) strains of Gram-negative bacteria causing nosocomial infection has become a serious concern in cancer patients. Therefore, the present study aimed to determine the spectrum and antibiotic resistance pattern of Gram-negative bacteria related nosocomial infections among Iranian cancer patients.

Materials and Methods:

This descriptive cross-sectional study was conducted during the 6 months from December 2015 to May 2016 in two tertiary care centers located in Isfahan and Arak Province. Gram-negative bacteria obtained from different clinical specimens from hospitalized patients with cancer and were identified using standard microbiological methods. Antibiotic susceptibility pattern was determined by the disk diffusion method according to the Clinical and Laboratory Standards Institute (CLSI) recommendation.

Results:

Of totally 259 culture positive cases, Escherichia coli showed the highest isolation rate (60.6%) followed by Klebsiella pneumoniae (26.6%) and Proteus spp (11.2%). The rate of MDR isolates were 91.5% (237/259). Overall, the most frequent source of bacterial isolation was urinary tract infection (65.6%) followed by skin and soft-tissue infection (23.6%). The antibiotic susceptibility results showed meropenem (MEN) and ceftazidime as the most effective antibiotics for E. coli, K. pneumoniae, and Proteus spp. isolates. Moreover, MEN was the most effective antibiotic against MDR isolates.

Conclusion:

The study findings showed a significant distribution of MDR Gram-negative bacteria which may increase the burden of healthcare-associated infections in cancer patients. Although, carbapenem can be considered as effective agents toward MDR strains for empirical antibiotic therapy in our region.

Evaluation of Biofilm Formation and Frequency of Multidrug-resistant and Extended Drug-resistant Strain in Pseudomonas aeruginosa Isolated from Burn Patients in Isfahan

Background:

Pseudomonas aeruginosa is a biofilm-forming bacterium which can result in serious health problems, particularly in burn patients. Biofilm has been assumed to protect the bacteria from environmental fluctuations such as antimicrobial agent. Mucoid strains generate extensive levels of the alginate exopolysaccharide, which is an important factor of its biofilm.

Materials and Methods:

Totally, 100 isolates of P. aeruginosa has been gathered from wound infections of burn patients. Polymerase chain reaction of exoA gene has been carried out to confirm the bacteriologic identification of isolates. The biofilm-forming capacity has been specified by capsule staining and microtiter plate test as qualitative and quantitative determination, respectively. Antimicrobial susceptibility of the isolates has been specified by disk diffusion method.

Results:

All the isolates carried the exoA gene. The antibiotic resistance was imipenem (90%); levofloxacin (93%); aztreonam (87%); piperacillin-tazobactam (85%); tobramycin (92%); polymyxin b (PB) (2%); and ceftazidime (CAZ) (32%). Totally, multidrug-resistant (MDR) and extended drug-resistant (XDR) isolates were 19% and 75%, respectively. Fortunately, pan drug-resistant (PDR) strain has not been observed. The assessment of biofilm formation has shown that 7% of the isolates were nonbiofilm (N), weak (W) 67%, moderate (M) 22%, and strong (S) 4%.

Conclusions:

As a result, the findings of this survey indicated that PB and CAZ were the most effective antibiotics against P. aeruginosa, which of course indicate a serious problem about the emergence of the PDR strains. There was no relationship between the patterns of biofilm production and antibiotic susceptibility, but high frequency of MDR/XDR and biofilm producer strains has been detected.

Genetic Diversity of Drug-resistant Mycobacterium tuberculosis Isolates in Isfahan Province of Iran

Background:

Increasing drug resistance is an important factor in the complexity of tuberculosis (TB) control. The identification of disease transmission type, recurrence of a previous infection, or new transmission of the disease is the key factor in the control of TB. In this study, we aimed to identify the genetic diversity of drug-resistant Mycobacterium tuberculosis isolates in Isfahan province of Iran through the mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) typing method based on 24 loci.

Materials and Methods:

Of 300 isolates obtained from a variety of clinical specimens, 18 drug-resistance M. tuberculosis clinical isolates (resistant to a single drug to more than one drug) were collected between 2013 and 2015 from regional TB reference laboratory in Isfahan. All drug-resistance M. tuberculosis isolates were typed by 24-locus MIRU-VNTR typing.

Results:

The highest percentage of isolates, 38.8%, belonged to the East-Asian lineage (lineage 2), while the lineages Indo-Oceanic (lineage 1), East-African–Indian (lineage 3), and Euro-American (lineage 4) represented 5.5%, 22.2%, and 33.3%, respectively. Among the 33.3% (6/18) Euro-American strains, the Latin American– Mediterranean and Ural sub-lineage were 22.2% (4/18) and 11.1% (2/18), respectively.

Conclusion:

The results of this study show that the lineages of drug-resistant M. tuberculosis isolates in Isfahan province of Iran are similar to those reported in the Eastern Mediterranean region (indicative of the epidemiological relationship between the countries in the region). Continued molecular monitoring is important as it has been proposed that the genetics and evolutionary backgrounds of drug-resistant M. tuberculosis strains may have an impact on the transmissibility profile.

Role of gut microbiota in the pathogenesis of colorectal cancer; a review article

Colorectal cancer (CRC) is one of the most frequently diagnosed cancers worldwide. Lifestyle is identified as one of the most important risk factors for CRC, especially in sporadic colorectal cancer. The natural composition of the gut microbiota changes rapidly during the first decade of life. Maintaining homeostasis in the gut is essential as structural and metabolic functions of the commensal microbiota inhibit gut colonization of pathogens. Dysbiosis, imbalance in function or structure of gut microbiota, has been associated with a variety of diseases, such as colorectal cancer. The aim of this review was to investigate the possible links between the dysbiosis in gut microbiota and colorectal cancer, and the potential role of anaerobic gut microbiota in the pathogenesis of colorectal cancer. Based on this review, various studies have shown that some of the gut microbiota such as anaerobic bacteria significantly increased in CRC patients, but we suggest more investigations are required to assess the importance of these bacteria and their metabolites in the pathogenesis of CRC are required.

Estimation of health risks caused by exposure to enteroviruses from agricultural application of wastewater effluents

Agricultural reuse of wastewater is a common practice worldwide, especially in arid and semiarid area due to the freshwater scarcity. Wastewater irrigation in the Middle East, one of the most water-stressed regions in the world, could be a key factor for socio-economic development, but the microbial contamination of untreated or partially treated wastewater is a serious public health concern. Potential transmission of enteric viral infections through wastewater reuse in agricultural activities represents a true health risk for exposed individuals. Accordingly, it is important to assess the health risks associated with wastewater reuse. A quantitative microbial risk assessment (QMRA) with Monte-Carlo simulation was used to estimate the annual risk of enterovirus (EV) infection and disease burden for farmers and consumers of wastewater-irrigated lettuce in Iran, a semiarid country in the Middle East region. Risk analysis was performed based on the measured concentrations of EV in effluent of two activated sludge wastewater treatment plants (WWTP). Wastewater effluent sampling was carried out over a nine-month period, and the presence of total and fecal coliforms and EV was determined. Fecal coliform bacteria were found at a high level exceeded the guideline limit for wastewater reuse in agriculture. EVs were detected in 40% of samples with the highest frequency in summer with a mean of 12 and 16 pfu/ml for WWTP-A and B, respectively. Statistical analysis showed no correlation between the concentration of fecal coliforms and EV. The estimated infection risk for EVs was 8.8 × 10-1 and 8.2 × 10-1 per person per year (pppy) for farmers of WWTP-A and -B, respectively which was about 2 log higher than the tolerable infection risk of 2 × 10-3 pppy. The estimated risk for lettuce consumers exhibited a lower level of infection and disease burden but higher than the guideline limits. The median disease burden for consumption of lettuce irrigated with activated sludge effluents was about 10-3 Disability Adjusted Life Years (DALY) pppy which exceeded the WHO guideline threshold of 10-4 DALY pppy. The results of study indicated that the activated sludge effluents require an additional reduction of EVs to achieve the acceptable level of risk for agricultural reuse of wastewater.

Optimal DNA Isolation Method for Detection of Nontuberculous Mycobacteria by Polymerase Chain Reaction

Background

Nontuberculous mycobacteria (NTM) are a group of opportunistic pathogens and these are widely dispersed in water and soil resources. Identification of mycobacteria isolates by conventional methods including biochemical tests, growth rates, colony pigmentation, and presence of acid-fast bacilli is widely used, but these methods are time-consuming, labor-intensive, and may sometimes remain inconclusive.

Materials and Methods

The DNA was extracted from NTM cultures using CTAB, Chelex, Chelex + Nonidet P-40, FTA^® Elute card, and boiling The quantity and quality of the DNA extracted via these methods were determined using UV-photometer at 260 and 280 nm, and polymerase chain reaction (PCR) amplification of the heat-shock protein 65 gene with serially diluted DNA samples.

Results

The CTAB method showed more positive results at 1:10-1:100,000 at which the DNA amount was substantial. With the Chelex method of DNA extraction, PCR amplification was detected at 1:10 and 1:1000 dilutions.

Conclusions

According to the electrophoresis results, the CTAB and Chelex DNA extraction methods were more successful in comparison with the others as regard producing suitable concentrations of DNA with the minimum use of PCR inhibitor.

Evaluation of Polymerase Chain Reaction for Detecting Coliform Bacteria in Drinking Water Sources

Background:

Coliform bacteria are used as indicator organisms for detecting fecal pollution in water. Traditional methods including microbial culture tests in lactose-containing media and enzyme-based tests for the detection of β-galactosidase; however, these methods are time-consuming and less specific. The aim of this study was to evaluate polymerase chain reaction (PCR) for detecting coliform.

Materials and Methods:

Totally, 100 of water samples from Isfahan drinking water source were collected. Coliform bacteria and Escherichia coli were detected in drinking water using LacZ and LamB genes in PCR method performed in comparison with biochemical tests for all samples.

Results:

Using phenotyping, 80 coliform isolates were found. The results of the biochemical tests illustrated 78.7% coliform bacteria and 21.2% E. coli. PCR results for LacZ and LamB genes were 67.5% and 17.5%, respectively.

Conclusion:

The PCR method was shown to be an effective, sensitive, and rapid method for detecting coliform and E. coli in drinking water from the Isfahan drinking water sources.

Targeting human breast cancer cells by an oncolytic adenovirus using microRNA-targeting strategy

MicroRNA-targeting strategy is a promising approach that enables oncolytic viruses to replicate in tumor cells but not in normal cells. In this study, we targeted adenoviral replication toward breast cancer cells by inserting ten complementary binding sites for miR-145-5p downstream of E1A gene. In addition, we evaluated the effect of increasing miR-145 binding sites on inhibition of virus replication. Ad5-control and adenoviruses carrying five or ten copies of miR145-5p target sites (Ad5-5miR145T, Ad5-10miR145T) were generated and inoculated into MDA-MB-453, BT-20, MCF-7 breast cancer cell lines and human mammary epithelial cells (HMEpC). Titer of Ad5-10miR145T in HMEpC was significantly lower than Ad5-control titer. Difference between the titer of these two viruses at 12, 24, 36, and 48h after infection was 1.25, 2.96, 3.06, and 3.77 log TCID₅₀. No significant difference was observed between the titer of both adenoviruses in MDA-MB-453, BT-20 and MCF-7 cells. The infectious titer of adenovirus containing 10 miR-145 binding sites in HMEpC cells at 24, 36, and 48h post-infection was 1.7, 2.08, and 4-fold, respectively, lower than the titer of adenovirus carrying 5 miR-145 targets. Our results suggest that miR-145-targeting strategy provides selectivity for adenovirus replication in breast cancer cells. Increasing the number of miRNA binding sites within the adenoviral genome confers more selectivity for viral replication in cancer cells.

Application of Epstein-Barr Virus for Optimization of Immortalized B-lymphocyte Production as a Positive Control in Genetic Studies

BACKGROUND

Infection of B-cells with Epstein-Barr virus (EBV) leads to more and subsequent immortalization. This is considered as the method of choice for generating lymphoblastoid cell lines (LCLs). Producing LCLs, although very useful but is very time consuming and troublesome, drives the requirement for quicker and more reliable methods for EBV-driven B-cell transformation.

MATERIALS AND METHODS

After successfully production of LCLs, different parameters including temperature, serum concentration, type of culture medium, and CO₂ concentration were evaluated on EBV-transformed B-cells. In this study, we were able to produce LCLs and optimize condition.

RESULTS

The best condition for generating LCLs was 37°C, 5% CO₂, 20% fasting blood sugar, and RPMI 1640. The study results were to establish a reliable method for producing LCLs that can be used to produce immortalized B-cells from almost any sources.

CONCLUSION

This can help with tumorgenecity studies, as well as producing control material for rare genetic disorders and so on. The aim of this study was to determine optimized condition for reliable and reproducible LCLs from different sources.

Distribution of the Strains of Multidrug-resistant, Extensively Drug-resistant, and Pandrug-resistant Pseudomonas aeruginosa Isolates from Burn Patients

Background:

Pseudomonas aeruginosa is an opportunistic and Gram-negative pathogen that is used as the most important factor in burn wound infections, and due to the rapid acquisition of multidrug resistance (MDR), it causes high mortality rates in these sectors. Thus, diagnosis and assessment of antibiotic resistance patterns are very important in these patients. The aim of this study was to evaluate antibiotic resistance pattern and determining P. aeruginosa MDR.

Materials and Methods:

In this study, phenotypic, biochemical, and polymerase chain reaction tests were used to identify P. aeruginosa from 120 wound burn samples that 96 samples were detected to P. aeruginosa species. In the next step, according to the Clinical and Laboratory Standard Institute standard guidelines, antibiogram test was performed by disk diffusion method for amikacin, ciprofloxacin, norfloxacin, gentamicin, cefepime, aztreonam, meropenem, colistin, ceftazidime, and piperacillin-tazobactam antibiotics. Antibiotic data were analyzed by WHONET software; finally, the rate of antibiotic resistance and MDR strains was determined.

Results:

The highest antibiotic resistance belonged to amikacin (94.8%) and norfloxacin (90.6%); in contrast, colistin (8.3%) had the lowest and the MDR strains were MDR (95.8%) and extensively drug resistance (XDR) (87.5%).

Conclusion:

In this study, there was MDR with an alarming rate including MDR (95.8%), XDR (87.5%), and pan-drug resistance (0%). As a result, given antibiotics to patients should be controlled by the antibiogram results to avoid increasing MDR strains.

Nosocomial Infections in Intensive Care Unit: Pattern of Antibiotic-resistance in Iranian Community

Background:

Bacterial infections are responsible for great number of mortality in Intensive Care Unit (ICU). Knowledge about prevalence of bacterial infections and their antibiotic-resistance pattern would be a great step for their treatment and management.

Materials and Methods:

Data about nosocomial infections in ICUs of Alzahra Hospital (referral hospital in Isfahan, center of Iran) were gathered during the years 2007–2010. A questionnaire was fulfilled for any specific patient with nosocomial infection containing demographic data of patient and also characteristics of the infection.

Results:

Out of all patients, 707 individuals (65.6%) were male and 370 (34.4%) were female. Our data revealed that Pseudomonas aeruginosa (13.9%), Klebsiella (11%), and Escherichia coli (6.4%) were the most prevalent bacterial infections. The most common sites of nosocomial infections in the ICU were respiratory system (399 cases, 37%), urinary system (230 cases, 21.4%), and blood (102 cases, 9.5%). The antibiotic-resistance of each bacteria in ICU ward was assessed and data were categorized in a table. There were less documentary about bacterial cultures in the year 2007 when compared with the next years.

Conclusion:

We found some differences (such as bacterial prevalence in ICU wards which caused nosocomial infections) in our local prevalence of nosocomial infections and also in their resistance pattern compared to other centers. Knowing about our data will help physicians to administer the most suitable antibiotics for treatment of nosocomial infections in our area.

The study of H. pylori putative candidate factors for single- and multi-component vaccine development

Helicobacter pylori has grown to colonize inside the stomach of nearly half of the world's population, turning into the most prevalent infections in the universe. Medical care failures noticeably confirm the need for a vaccine to hinder or deal with H. pylori. This review is planned to discuss the most known factors as a vaccine candidate, including single (AhpC, BG, CagA, KatA, Fla, Hsp, HWC, Lpp, LPS, NAP, OMP, OMV, SOD, Tpx, Urease, VacA) and multi-component vaccines. Many promising results in the field of single and multivalent vaccine can be seen, but there is no satisfactory outcome and neither a prophylactic nor a therapeutic vaccine to treat or eradicate the infection in human has been acquired. Hence, selecting suitable antigen is an important factor as an appropriate adjuvant. Taken all together, the development of efficient anti-H. pylori vaccines relies on the fully understanding of the interactions between H. pylori and its host immune system. Therefore, more work should be done on epitope mapping, analysis of molecular structure, and determination of the antigen determinant region as well due to design a vaccine, preferably a multi-component vaccine to elicit specific CD4 T-cell responses that are required for H. pylori vaccine efficacy.

Isolation of bacteriophages against multidrug resistant Acinetobacter baumannii

Increasing multiple drug resistant (MDR) strains of Acinetobacter baumannii has aggravated curiosity in development of alternative therapy. Bacteriophages are often considered as alternative agents for controlling A. baumannii infections. In the present study two lytic phages for MDR A. baumannii were isolated and their efficacy and host ranges were evaluated. The phages were isolated from hospital wastewater. Electron microscopy revealed that IsfAB78 might belong to Myoviridae and IsfAB39 to Podoviridae. Initial characterization of phages showed that they have narrow host range and failed to infect relative and non-relative bacteria. Both phages decreased the A. baumannii turbidity significantly, indicating that these isolated phages may be considered as candidates for phage therapy.

Genetic Lineages of Mycobacterium tuberculosis Isolates in Isfahan, Iran

In this study, we aimed to identify the genetic lineages of Mycobacterium tuberculosis isolates in Isfahan via the mycobacterial interspersed repetitive-unit-variable number tandem repeat typing method based on 15 loci. Forty-nine M. tuberculosis isolates were collected between 2013 and 2015 from Tuberculosis patients in Mollahadi Sabzevari Tuberculosis Center in Isfahan. All isolates were typed by 15-locus MIRU-VNTR typing. The highest percentage of isolates, 44.89 % (22/49), belonged to the Euro-American lineage, while the frequencies of the East-African-Indian, East-Asian, and Indo-Oceanic lineages were 28.57 % (14/49), 24.4 % (12/49), and 2.04 % (1/49), respectively. Among the 22 isolates of the Euro-American lineage, those belonging to the NEW-1 sub-lineage were most prevalent (24.4 %). Approximately, the same proportion of isolates belonging to the Delhi/CAS, Beijing, and NEW-1 sub-lineages were identified in Iranian and Afghan immigrant patients. The Delhi/CAS and Beijing sub-lineage isolates were prevalent among patients who had been previously treated for TB. Results showed that all of the 49 MIRU-VNTR patterns were unique and the clustering rate of the 15-locus MIRU-VNTR was 0.0 (minimum recent transmission). The results of this study show that the lineages of M. tuberculosis isolates in Isfahan are similar to those reported in the Eastern Mediterranean region (indicative of the epidemiological relationship between the countries in the region). The low clustering rate in our results reveals that transmission of tuberculosis in Isfahan is, in most cases, a reactivation of previous tuberculosis infection and the role of recently transmitted disease is minor.

Selective replication of miR-145-regulated oncolytic adenovirus in MCF-7 breast cancer cells

Aim: Selective replication of oncolytic viruses in cancer cells is a challenge in virotherapy. miRNA-145 is downregulated in breast cancer cell lines and cancer tissues. In order to target replication of the oncolytic adenovirus 5 in breast cancer cells, we constructed a miRNA-145-regulated oncolytic adenovirus (AD5-miR-145-5pT) by inserting five copies of the miR-145-5p target sites into the 3′-untranslated region of E1A gene. Materials & methods: The MCF-7 human breast cancer cell line and the normal human mammary epithelial cells (HMEpC) were infected with AD5-miR145-5pT, and then the viral titers were measured 12, 24, 36 and 48 h postinfection using TCID50 assay. Results: Growth kinetic analysis of AD5-miR-145-5pT in MCF-7 cells and HMEpC showed that replication of the engineered adenovirus was inhibited in HMEpC as normal breast cells, whereas the virus efficiently replicated in MCF-7 cells. Infectious titer of AD5-miR-145-5pT at 48 h postinfection in HMEpC was 3.2 log TCID50 lower than that of the AD5-control. Conclusion: These results suggest that AD5-miR-145-5pT may be a feasible approach for the targeting of breast cancer cells and other cancers where the miRNA-145 is downregulated. miR-145-5p can be applied to miR-targeting of other oncolytic viruses toward breast carcinoma cells.

Evaluation of the effect of Pulicaria gnaphalodes and Perovskia abrotanoides essential oil extracts against Mycobacterium tuberculosis strains

Background:

Mycobacterium tuberculosis (MTB) is the causative agent of tuberculosis (TB), which remains one of the major public health problems in the world. The increasing incidence of multidrug-resistant tuberculosis (MDR-TB) and extensively drug-resistant tuberculosis (XDR-TB) worldwide highlights the urgent need to search for alternative antimycobacterial agents. More and more people in developing countries utilize traditional medicine for their major primary health care needs. It has been determined that the medicinal plants Pulicaria gnaphalodes and Perovskia abrotanoides possess strong antibacterial effect.

Materials and Methods:

In this study, the antimycobacterial effects of P. gnaphalodes and P. abrotanoides essential oil on MTB were examined. Essential oil was prepared from P. gnaphalodes aerial parts and P. abrotanoides flower. The effects of six different concentrations (20 μg/ml, 40 μg/ml, 80 μg/ml, 160 μg/ml, 320 μg/ml, and 640 μg/ml) were examined against sensitive isolates of MTB and MTB H37Rv (ATCC 27294).

Results:

The results showed that P. gnaphalodes and P. abrotanoides essential oil extracts have strong inhibitory effects on MTB. This activity for P. gnaphalodes was observed from very low (4%) to good (70.9%) effect; meanwhile, this activity for P. abrotanoides was observed from very low (4%) to strong (86%) effect.

Conclusion:

The mean of inhibition percentage for P. gnaphalodes and P. abrotanoides in 640 μg/ml was 58.1% and 76.2%, respectively. So, P. abrotanoides plant is more effective against MTB than P. gnaphalodes. Identification of the effective fraction against MTB is a further step to be studied.

Phylogenetic Analysis of Prevalent Tuberculosis and Non-Tuberculosis Mycobacteria in Isfahan, Iran, Based on a 360 bp Sequence of the rpoB Gene

Background

Taxonomic and phylogenetic studies of Mycobacterium species have been based around the 16sRNA gene for many years. However, due to the high strain similarity between species in the Mycobacterium genus (94.3% - 100%), defining a valid phylogenetic tree is difficult; consequently, its use in estimating the boundaries between species is limited. The sequence of the rpoB gene makes it an appropriate gene for phylogenetic analysis, especially in bacteria with limited variation.

Objectives

In the present study, a 360bp sequence of rpoB was used for precise classification of Mycobacterium strains isolated in Isfahan, Iran.

Materials and Methods

From February to October 2013, 57 clinical and environmental isolates were collected, subcultured, and identified by phenotypic methods. After DNA extraction, a 360bp fragment was PCR-amplified and sequenced. The phylogenetic tree was constructed based on consensus sequence data, using MEGA5 software.

Results

Slow and fast-growing groups of the Mycobacterium strains were clearly differentiated based on the constructed tree of 56 common Mycobacterium isolates. Each species with a unique title in the tree was identified; in total, 13 nods with a bootstrap value of over 50% were supported. Among the slow-growing group was Mycobacterium kansasii, with M. tuberculosis in a cluster with a bootstrap value of 98% and M. gordonae in another cluster with a bootstrap value of 90%. In the fast-growing group, one cluster with a bootstrap value of 89% was defined, including all fast-growing members present in this study.

Conclusions

The results suggest that only the application of the rpoB gene sequence is sufficient for taxonomic categorization and definition of a new Mycobacterium species, due to its high resolution power and proper variation in its sequence (85% - 100%); the resulting tree has high validity.

Analysis of DNA gyrA Gene Mutation in Clinical and Environmental Ciprofloxacin-Resistant Isolates of Non-Tuberculous Mycobacteria Using Molecular Methods

Background

During the past several years, nontuberculous mycobacteria (NTM) have been reported as some of the most important agents of infection in immunocompromised patients.

Objectives

The aim of this study was to evaluate the ciprofloxacin susceptibility of clinical and environmental NTM species isolated from Isfahan province, Iran, using the agar dilution method, and to perform an analysis of gyrA gene-related ciprofloxacin resistance.

Materials and Methods

A total of 41 clinical and environmental isolates of NTM were identified by conventional and multiplex PCR techniques. The isolates were separated out of water, blood, abscess, and bronchial samples. The susceptibility of the isolates to 1 µg/mL, 2 µg/mL and 4 µg/mL of ciprofloxacin concentrations was determined by the agar dilution method according to CLSI guidelines. A 120-bp area of the gyrA gene was amplified, and PCR-SSCP templates were defined using polyacrylamide gel electrophoresis. The 120-bp of gyrA amplicons with different PCR-SSCP patterns were sequenced.

Results

The frequency of the identified isolates was as follows: Mycobacterium fortuitum, 27 cases; M. gordonae, 10 cases; M. smegmatis, one case; M. conceptionense, one case; and M. abscessus, two cases. All isolates except for M. abscessus were sensitive to all three concentrations of ciprofloxacin. The PCR-SSCP pattern of the gyrA gene of resistant M. abscessus isolates showed four different bands. The gyrA sequencing of resistant M. abscessus isolates showed 12 alterations in nucleotides compared to the M. abscessus ATCC 19977 resistant strain; however, the amino acid sequences were similar.

Conclusions

This study demonstrated the specificity and sensitivity of the PCR-SSCP method for finding mutations in the gyrA gene. Due to the sensitivity of most isolates to ciprofloxacin, this antibiotic should be considered an appropriate drug for the treatment of related diseases.

Morphological and Bactericidal Effects of Amikacin, Meropenem and Imipenem on Pseudomonas aeruginosa

Background:

Pseudomonas aeruginosa might be converted to coccoid bacteria under antibiotic stress. Bacterial conversion would increase resistance to antibiotics due to changes in cell wall crosslink or decreased metabolic activity. Morphology of P. aeruginosa under stress conditions (presence of antibiotics) can be changed to elongated bacilli, U shape and finally coccoid bacteria. Results of several researches showed that coccoid bacteria are one of the most important aspects of drug resistance. It would be the major reason for treatment failure.

Objectives:

The aim of this study was to determine in vitro morphological and bactericidal effects of amikacin, meropenem and imipenem on P. aeruginosa isolated from clinical specimens.

Materials and Methods:

Eight P. aeruginosa isolates obtained from clinical samples of burned patients and standard strain ATCC 27853 were used in this study. Isolates were identified by biochemical tests and confirmed by PCR method using ITS specific primer. Minimum inhibitory concentrations (MICs) of three antibiotics were determined by E-test method. Bacteria were exposed to antibiotics at different concentrations. Bacterial morphology in different days was examined by specific microscope and viability of isolates was examined by flow cytometry

Results:

All used antibiotics at sub MIC concentration had capability to induce coccoid bacteria. The highest rate of induced coccoid bacteria was 98.2% after 8 days, with contribution of imipenem and meropenem at 2 μg/mL concentration. Amikacin at 4 μg/mL concentration induced lower rate of coccoid bacteria (55.05%). Amikacin had a strong bactericidal effect on coccoid bacteria at 8 μg/mL concentration. Imipenem and meropenem showed very weak bactericidal effect on coccoid bacteria.

Conclusions:

Induction of coccoid form of P. aeruginosa may be one of the important reasons for antibiotic treatment failure; therefore, prescribed dose of antibiotics should be carefully managed to prevent increasing antibiotic resistance and coccoid bacteria induction.

The Bioinformatics Report of Mutation Outcome on NADPH Flavin Oxidoreductase Protein Sequence in Clinical Isolates of H. pylori

frxA gene has been implicated in the metronidazole nitro reduction by H. pylori. Alternatively, frxA is expected to contribute to the protection of urease and to the in vivo survival of H. pylori. The aim of present study is to report the mutation effects on the frxA protein sequence in clinical isolates of H. pylori in our community. Metronidazole resistance was proven in 27 of 48 isolates. glmM and frxA genes were used for molecular confirmation of H. pylori isolates. The primer set for detection of whole sequence of frxA gene for the effect of mutation on protein sequence was used. DNA and protein sequence evaluation and analysis were done by blast, Clustal Omega, and T COFFEE programs. Then, FrxA protein sequences from six metronidazole-resistant clinical isolates were analyzed by web-based bioinformatics tools. The result of six metronidazole-resistant clinical isolates in comparison with strain 26695 showed ten missense mutations. The result with the STRING program revealed that no change was seen after alterations in these sequences. According to consensus data involving four methods, residue substitutions at 40, 13, and 141 increase the stability of protein sequence after mutation, while other alterations decrease. Residue substitutions at 40, 43, 141, 138, 169, and 179 are deleterious, while, V7I, Q10R, V34I, and V96I alterations are neutral. As FrxA contribute to survival of bacterium and in regard to the effect of mutations on protein function, it might affect the survival and bacterium phenotype and it need to be studied more. Also, none of the stability prediction tool is perfect; iStable is the best predictor method among all methods.

Production of IFN-γ and IL-4 Against Intact Catalase and Constructed Catalase Epitopes of Helicobacter pylori From T-Cells

Background:

Helicobacter pylori infection is highly prevalent in the developing countries. It causes gastritis, peptic ulcer disease, and gastrocarcinoma. Treatment with drugs and antibiotics is problematic due to the following reasons: cost, resistance to antibiotics, prolonged treatment and using multiple drugs. Catalase is highly conserved among the Helicobacter species and is important to the survival of the organism. It is expressed in high amounts and is exposed to the surface of this bacterium; therefore it represents a suitable candidate vaccine antigen.

Objectives:

A suitable approach in H. pylori vaccinology is the administration of epitope based vaccines. Therefore the responses of T-cells (IFN-γ and IL-4 production) against the catalase of H. pylori were determined. Then the quality of the immune responses against intact catalase and three epitopes of catalase were compared.

Materials and Methods:

In this study, a composition of three epitopes of the H. pylori catalase was selected based on Propred software. The effect of catalase epitopes on T-cells were assayed and immune responses identified.

Results:

The results of IFN-γ, IL-4 production against antigens, epitopes, and recombinant catalase by T-cells were compared for better understanding of epitope efficiency.

Conclusions:

The current research demonstrated that epitope sequence stimulates cellular immune responses effectively. In addition, increased safety and potency as well as a reduction in time and cost were advantages of this method. Authors are going to use this sequence as a suitable vaccine candidate for further research on animal models and humans in future.

Sewage sludge composting: quality assessment for agricultural application

In order to use sewage sludge (SS) composts in agriculture, it is extremely important to estimate the quality of compost products. The aim of this study was to investigate the quality of composted SS as a fertilizer and soil amendment especially in semi-arid areas. To determine the quality and agronomic value of the SS compost products, analyses on pH, electrical conductivity, organic matter content, C/N ratio, phytotoxicity, microbial load, and heavy metal content of composted anaerobically digested SS, with different proportions (1:1, 1:2, and 1:3 v/v) of green and dry plant waste, as bulking agents, were performed. The 1:2 and 1:3 mixtures of SS and green/dry plant waste were the most beneficial for composting, with final composts attaining high organic matter degradation and exhibiting low amounts of heavy metals, a relatively high germination index, and significant reduction of pathogens, suggesting the agricultural relevance of composted SS and green/dry plant waste at 1:2 and 1:3 (v/v) proportions. pH and electrical conductivity were also within the permissible limits. With respect to international standards, it appears that composted SS and green/dry plant waste at 1:2 and 1:3 proportions pose no threat to soil or plant quality if used in agriculture or land restoration.

Molecular typing of Iranian mycobacteria isolates by polymerase chain reaction-restriction fragment length polymorphism analysis of 360-bp rpoB gene

Background:

Diagnosis and typing of Mycobacterium genus provides basic tools for investigating the epidemiology and pathogenesis of this group of bacteria. Polymerase chain reaction (PCR)-restriction fragment length polymorphism analysis (PRA) is an accurate method providing diagnosis and typing of species of mycobacteria. The present study is conducted by the purpose of determining restriction fragment profiles of common types of mycobacteria by PRA method of rpoB gene in this geographical region.

Materials and Methods:

Totally 60 clinical and environmental isolates from February to October, 2013 were collected and subcultured and identified by phenotypic methods. A 360 bp fragment of the rpoB gene amplified by PCR and products were digested by MspI and HaeIII enzymes.

Results:

In the present study, of all mycobacteria isolates identified by PRA method, 13 isolates (21.66%) were Mycobacterium tuberculosis, 34 isolates (56.66%) were rapidly growing Nontuberculosis Mycobacteria (NTM) that including 26 clinical isolates (43.33%) and 8 environmental isolates (13.33%), 11 isolates (18.33%) were clinical slowly growing NTM. among the clinical NTM isolates, Mycobacterium fortuitum Type I with the frequency of 57.77% was the most prevalent type isolates. Furthermore, an unrecorded of the PRA pattern of Mycobacterium conceptionense (HeaIII: 120/90/80, MspI: 120/105/80) was found. This study demonstrated that the PRA method was high discriminatory power for identification and typing of mycobacteria species and was able to identify 96.6% of all isolates.

Conclusion:

Based on the result of this study, rpoB gene could be a potentially useful tool for identification and investigation of molecular epidemiology of mycobacterial species.

Antibiotic Resistance Patterns and Genetic Diversity in Clinical Isolates of Pseudomonas aeruginosa Isolated From Patients of a Referral Hospital, Isfahan, Iran

Background:

Pseudomonas aeruginosa is a well-known opportunistic pathogen, which affects hospitalized patients in different wards due to its natural resistance to drugs.

Objectives:

The purpose of the current study was to determine the antibiotic susceptibility profiles and genetic relatedness in P. aeruginosa isolated from patients admitted to a referral hospital in Isfahan, Iran.

Materials and Methods:

Out of 150 analyzed samples, 54 P. aeruginosa isolates were recovered and were subjected to antibiotic resistance patterns and genetic diversity determination by Kirby-Bauer’s disk diffusion method and RAPD-PCR, respectively.

Results:

The highest percentage of resistance was observed against ceftazidime and imipenem with 30 (55.6%) isolates; meanwhile all isolates were sensitive to polymyxin B. Twenty-eight (51.8%) isolates revealed resistance to all applied antibiotics. RAPD-PCR (Random Amplified Polymorphic DNA- Polymerase Chain Reaction) results showed 54 unique genotypes, which were divided into 39 clusters.

Conclusions:

Although different source of P. aeruginosa may involve in patient colonization, genetically related strains were isolated from different wards and or the same ward of the hospital. Our results pointed to the restriction of currently used antibiotics in studied hospital. We hope that our results cast light on the control and transmission of the infection in the investigated hospital.

Molecular identification of Acinetobacter baumannii isolated from intensive care units and their antimicrobial resistance patterns

Background:

Acinetobacter baumannii is one of the most important pathogens in hospital-acquired infections especially in intensive care units (ICUs). This opportunistic pathogen can be easily isolated from water, soil, and hospital facilities. A. baumannii as a nosocomial opportunistic pathogen is resistant to a wide range of antibiotics and responsible for multiple infections, including bacteremia, pneumonia, meningitis, urinary tract infections, and surgical wounds. The aim of this study was to determine frequency and resistance patterns of A. baumannii isolated in ICUs of Isfahan Hospitals.

Materials and Methods:

During 1 year period (2012-2013), 350 specimens were collected from ICUs of Isfahan hospitals. The isolates were characterized as A. baumannii by conventional phenotypic, biochemical tests and confirmed by PCR for OXA-51-like gene. Susceptibility of isolates was determined by standard disk diffusion method according to CLSI.

Results:

From total of 350 specimens, 43 isolates were A. baumannii. The antimicrobial patterns of isolates showed that 53.5% of isolates were resistant to amikacin, 83.7% to tetracyclin, 86% to ceftazidime, 90.7% to Trimethoprim sulfametoxazol, 93% to imipenem, cefepime, meropenem, ampicillin–sulbactam. All isolates were resistant to ciprofloxacin.

Conclusion:

This study showed a high resistance of A. baumannii to a wide range of antimicrobial agent. It is necessary to adopt appropriate strategies to control the spread of the bacteria in care unit centers and wards.