Comparative analysis of the root and leaf transcriptomes in Chelidonium majus L.

Chelidonium majus is a traditional medicinal plant, which commonly known as a rich resource for the major benzylisoquinoline alkaloids (BIAs), including morphine, sanguinarine, and berberine. To understand the biosynthesis of C. majus BIAs, we performed de novo transcriptome sequencing of its leaf and root tissues using Illumina technology. Following comprehensive evaluation of de novo transcriptome assemblies produced with five programs including Trinity, Bridger, BinPacker, IDBA-tran, and Velvet/Oases using a series of k-mer sizes (from 25 to 91), BinPacker was found to produce the best assembly using a k-mer of 25. This study reports the results of differential gene expression (DGE), functional annotation, gene ontology (GO) analysis, classification of transcription factor (TF)s, and SSR and miRNA discovery. Our DGE analysis identified 6,028 transcripts that were up-regulated in the leaf, and 4,722 transcripts that were up-regulated in the root. Further investigations showed that most of the genes involved in the BIA biosynthetic pathway are significantly expressed in the root compared to the leaf. GO analysis showed that the predominant GO domain is "cellular component", while TF analysis found bHLH to be the most highly represented TF family. Our study further identified 10 SSRs, out of a total of 39,841, that showed linkage to five unigenes encoding enzymes in the BIA pathway, and 10 conserved miRNAs that were previously not detected in this plant. The comprehensive transcriptome information presented herein provides a foundation for further explorations on study of the molecular mechanisms of BIA synthesis in C. majus.

Isolation and identification of the native population bacteria for bioremediation of high levels of arsenic from water resources.

Health of millions of people is threatened by the risk of drinking arsenic-contaminated water worldwide. Arsenic naturally conflicts with the concept of life, but recent studies showed that some microorganisms use toxic minerals as the source of energy. Hence, the researchers should consider the development of cost-effective and highly productive procedures to remove arsenic. The current study was conducted on a native bacterial population of Seyed-Jalaleddin Spring Kurdistan, Iran. Accordingly, the arsenic amount in water samples was measured >500 µg/L by the two field and in vitro methods. Water samples were transferred to laboratory and cultured on chemically defined medium (CDM) with arsenic salts. A total of 14 native arsenic-resistant bacterial strains were isolated and after providing pure culture and performing biochemical tests, the isolates were identified using polymerase chain reaction (PCR) and 16s rRNA genomic sequencing. The potential of bacterial strains for the biotransformation of arsenic was assessed by the qualitative assessment of AgNO3 method and efficiency of arsenic speciation was determined for the first time by silver diethyldithiocarbamate (SDDC) method with an error of less than 5%. Among the isolated strains, only strain As-11 and strain As-12 showed arsenic transformation characteristics and were registered in NCBI database by the access numbers KY119262 and KY119261, respectively. Results of the current study indicated that strain As-11 had the potential of biotransformation of As(V) to As(III) and vice versa with the efficiency of 78% and 48%, respectively. On the other hand, strain As-12 had the potential for biotransformation of As(V) to As(III) and vice versa with the efficiency of 28% and 45%, respectively.

Pilus-encoding islets in S. agalactiae and its association with antibacterial resistance and serotype distribution.

Group B Streptococcus (GBS) is a versatile organism which uses multiple virulence factors which bind to the surface of epithelial cells. Pili are one of virulence factors detected in recent years. A total of 90 isolates were collected from invasive and non-invasive isolates among adults throughout 2014-2015. Isolates were serotyped at molecular level based on capsular polysaccharide (cps) serotyping and analyzed for pilus island profiles, scpB gene, and hvgA gene presence. Isolates were subjected to antimicrobial susceptibility towards penicillin, tetracycline, erythromycin, clindamycin, moxifloxacin, levofloxacin, and vancomycin by disk diffusion method and MICs for erythromycin and clindamycin were determined by broth dilution methods. Overall, 4 serotypes were identified, serotype III (68.88%), V (20%), II (10%) and Ib (1.11%) and hvgA gene was detected in 7.7% (n = 7) of the isolates; all were serotype III/ST 17. All isolates were susceptible to penicillin and vancomycin, except one isolate which showed intermediate resistance to penicillin and other complete resistance to vancomycin. Isolates were resistant to tetracycline (98%), erythromycin (25%), clindamycin (22%), moxifloxacin (8%), and levofloxacin (6%). The scpB gene was detected in all isolates, while isolates harbored at least one PI, of which the PI-1+PI-2a was the most frequent combination observed. Our data show the presence of the relation between serotype or pilus genes among clinical isolates of Streptococcus agalactiae. These data are principal to help in designing prevention and treatment strategies for GBS infections in the region.

Genotyping and Phylogenetic Analysis of Group B Streptococcus by Multiple Locus Variable Number Tandem Repeat Analysis in Iran.

BACKGROUND: Group B streptococcus (GBS), also known as Streptococcus agalactiae, is well known as a causative agent for neonatal invasive diseases; it is also a major pathogen in adults. Analytic epidemiology is required to monitor the clinical isolates of GBS. However, there is insufficient information on the genetic background of GBS in Iran, and this information is needed to guide and develop a GBS vaccine. MATERIALS AND METHODS: In total, 90 well-char - acterized GBS isolates were collected from April 2014 to August 2015. In this study, molecular typing was used to disclose a relationship between the multiple-locus variable number tandem repeat analysis (MLVA) types, serotyping, and pilus islands. The isolates were characterized by the types of capsular polysaccharides and pilus islands and were examined by MLVA to study the epidemiological relationship of isolates. RESULTS: The results indicate that there is a significant relationship between the distribution of serotypes and pilus island genes; GBS isolates were differentiated into 12 types by capsular polysaccharides and pilus islands analysis. The discriminatory power of an MLVA analysis was high based on the five most variable numbers of tandem repeat loci and 44 MLVA types that were identified. CONCLUSION: This study has provided useful insights into the genetic heterogeneity of GBS isolates in Tehran and Alborz, Iran. The extensive distribution of pilus islands in various serotypes and MLVA types throughout the GBS population refers to the advancement of the pilus-based GBS vaccines.

Isolation and identification of indigenous prokaryotic bacteria from arsenic-contaminated water resources and their impact on arsenic transformation.

Arsenic is a known human carcinogen. Arsenite [As(III), H3AsO3] and arsenate [As(V), H2AsO4- and HAsO42-] are the two predominant compounds of As found in surface water and groundwater. The aim of this study was to explore a bioremediation strategy for biotransformation of arsenite to arsenate by microorganisms. In this study, Babagorgor Spring, located west of Iran, was selected as the arsenic-contaminated source and its physicochemical characteristics and in situ microbiological composition were analyzed. Inductively Coupled Plasma-Atomic Emission Spectrometry (ICP-AES) analysis indicated that the arsenic level was 614µg/l. Fourteen arsenic tolerant indigenous bacteria were isolated from arsenic-contaminated water using chemically defined medium (CDM), supplemented with 260-3900mg/l arsenite and 1560-21800mg/l arsenate. Among the isolates, a strain As-11 exhibited high ability of arsenic transformation. Biochemical tests were used for bacterial identification and confirmation was conducted by 16S rRNA sequence analysis. Results confirmed that As-11 was related to the genus Pseudomonas. This bacterium showed maximum tolerable concentration to arsenite up to 3250mg/l and arsenate up to 20280mg/l. Under heterotrophic conditions, the bacterium exhibited 48% of As(III) and 78% of As(V) transformation from the medium amended with 130 and 312mg/l of sodium arsenite and sodium arsenate, respectively. Moreover, under chemolithotrophic conditions, bacterium was able to transform 41% of 130mg/l of As(III) from the medium amended with nitrate as the terminal electron acceptor. Pseudomonas strain As-11 was reported as an arsenic transformer, for the first time.

Prevalence of chronic viral hepatitis infections in Karaj, Iran.

INTRODUCTION: Viral hepatitis is challenging for health and blood safety. Studies carried out on blood donors can help find the frequency and trending of hepatitis B and C infections in a community and also safety of donation. The study aim is to determine the prevalence of HBV and HCV in Karaj blood donors over a four year period between 2010 to 2013. METHODS: This study reports the results of a cross sectional seroepidemiological study of hepatitis B and C in blood donors. Data on hepatitis infection and demographic characteristics of donors were gathered from blood donor registries. Frequency of hepatitis infections were described with 95% confidence interval. Chi square and logistic regression were used for analysis. RESULTS: The frequency of HBV and HCV infection in Karaj blood donors was 0.40% and 0.18% respectively. In first time donors, HBV and HCV positivity risk was respectively 3.59 and 4.8 fold in people with primary education (OR=3.59; 95% CI between 2.68-4.80) comparing to academic level. Frequency of hepatitis B has decreased significantly (P<0.001) during study period but frequency of Hepatitis C has not changed significantly. CONCLUSION: The frequencies of HBV and HCV infection in Karaj blood donor population is low. There are equal infection rates within both genders. This must be considered in controlling transmission of infection in this area.

Bacillus flexus strain As-12, a new arsenic transformer bacterium isolated from contaminated water resources.

A total of 14 arsenic-resistant bacteria were isolated from an arsenic-contaminated travertine spring water in the central district of Qorveh county, Kurdistan Province, Iran. One of strains designated As-12 was selected for further investigation because of its ability to transform arsenic. The strain was identified by cultural, morphological and biochemical tests, and 16S rRNA gene sequencing. Finally, the growth characteristics of the isolate were investigated in a chemically defined medium which included varied ranges of environmental factors such as pH, temperature and salinity. Moreover, the resistance of this strain to some heavy metals was evaluated. The bacterium was a Gram-positive, endospore-forming with all other characteristics of the genus Bacillus. It revealed maximum similarity at the 16S rRNA gene level with Bacillus flexus. The optimum growth of the strain was observed at 38 °C, pH 9 and 2% salinity. This strain was resistant to heavy metals such as zinc, chromium, lead, nickel, copper, mercuric and cadmium at concentrations of 15 mM, 15.5 mM, 11.5 mM, 12 mM, 11 mM, 5.5 mM, and 1 mM, respectively. The isolated bacterium was able to reduce As (V) to As (III) (about 28%) and oxidize As (III) to As (V) (about 45%) after 48 h of incubation at 37 °C. In conclusion, Bacillus flexus strain As-12, was identified as an arsenic transformer, for the first time.

Biodegradation of 2,4-dichlorophenoxyacetic acid by bacteria with highly antibiotic-resistant pattern isolated from wheat field soils in Kurdistan, Iran.

Recently, there has been increasing interest to clean up the soils contaminated with herbicide. Our aim was to determine the bioremediation of 2,4-dichlorophenoxyacetic acid (2,4-D) from wheat fields which have a long history of herbicide in Sanandaj. Based on our literature survey, this study is the first report to isolate and identify antimicrobial resistant bacteria from polluted wheat field soils in Sanandaj which has the capacity to degrade 2,4-D. From 150 2,4-D-exposed soil samples, five different bacteria were isolated and identified based on biochemical tests and 16S ribosomal RNA (rRNA). Pseudomonas has been the most frequently isolated genus. By sequencing the 16S rRNA gene of the isolated bacteria, the strains were detected and identified as a member of the genus Pseudomonas sp, Entrobacter sp, Bacillus sp, Seratia sp, and Staphylococcus sp. The sequence of Sanandaj 1 isolate displayed 87% similarity with the 16S rRNA gene of a Pseudomonas sp (HE995788). Similarly, all the isolates were compared to standard strains based on 16S rRNA. Small amounts of 2,4-D could be transmitted to a depth of 10-20 cm; however, in the depth of 20-40 cm, we could not detect the 2,4-D. The isolates were resistant to various antibiotics particularly, penicillin, ampicillin, and amoxicillin.

First experience of Candida non-albicans isolates with high antibiotic resistance pattern caused oropharyngeal candidiasis among cancer patients.

BACKGROUND AND AIM: In cancer patients, Candida species can cause a variety of diseases particularly oropharyngeal candidiasis which is a common infection. In this study, an attempt has been made to determine susceptibility pattern of four antifungal agents against the Candida species isolated from cancer patients with oropharyngeal candidiasis. MATERIALS AND METHODS: Samples were taken from 50 cancer patients with oropharyngeal candidiasis by the physician, and isolation and identification of Candida spp. was done based on standard procedures. Antifungal resistance pattern was carried out according to CLSI guidelines, and 18s ribosomal RNA among Candida spp. was identified using multiplex polymerase chain reaction. RESULTS: Of the 50 patients, 18 (36%) were females and 32 (64%) were males; mean age was 38.4 years. Leukemia and lymphoma were the most frequent cancer types in the studied group, accounting for 17 (34%) and 12 (24%), respectively. A total of 29 Candida spp. were isolated from 29 cancer patients, of which 17 were C. albicans and 12 were C. non-albicans. All the Candida spp. were confirmed having 18s ribosomal RNA. Among all the Candida spp., C. non-albicans showed higher resistance pattern to amphotericin B (MIC 07 µg/ml) and ketoconazole (MIC = 05 µg/ml). CONCLUSION: In conclusion, oropharyngeal Candidiasis is a serious infection among cancer patients. The isolated Candida spp. were resistant to common antifungal agents, which may lead to longer hospital stay, more expensive/toxic drugs and higher mortality. Therefore, interval surveillance is necessary in developing institutional guidelines.

Prevalence and Antibiotic Susceptibility Patterns of Extended-Spectrum ß-Lactamase and Metallo-ß-Lactamase-Producing Uropathogenic Escherichia coli Isolates.

Healthcare professionals worldwide have expressed concern over infections by extended-spectrum ß-lactamase (ESBL) and metallo-ß-lactamase (MBL)-producing bacteria. We evaluated the prevalence of ESBL- and MBL-producing Escherichia coli (E. coli) isolated from community-acquired urinary tract infections (UTIs) and their antibiotic-resistance profiles at 3 private laboratories in Tehran, Iran. E. coli isolates were mostly susceptible to meropenem (90.4%) and imipenem (90.0%), followed by amikacin (89.0%) and gentamicin (84.7%). Moreover, we detected that, of the E. coli isolates, 67 (22.3%) were ESBL producers and 21 (7.0%) of E. coli isolates were MBL positive via the imipenem-ethylenediaminetetraacetic acid (EDTA) combined disc test. This report is the first, to our knowledge, on the prevalence of MBL-producing uropathogenic E. coli (UPEC) strains in Iran. The antibiotic resistance of E. coli isolates revealed that 122 (40.7%) were multidrug resistant. The high number of antibiotic-resistant and ß-lactamase-producing UPEC strains necessitates further attention and consideration, particularly MBL-producing strains.

Isolation and antibiotic susceptibility of Shigella species from stool samples among hospitalized children in Abadan, Iran.

AIM: The aim of this study was to determine the incidence of Shigella species and their antimicrobial susceptibility patterns in hospitalized children with Shigellosis in Abadan, Iran. BACKGROUND: Shigellosis is caused by different species of Shigella and one of the most common causes of diarrhea in children. This disease is endemic in many developing countries including Iran. PATIENTS AND METHODS: This prospective cross sectional study was conducted in a teaching hospital in Abadan, Iran during June 2011 to May 2013. Stool specimens were collected from pediatric age group. All isolates were confirmed as Shigella species by biochemical and serologic tests. Antibiotic sensitivity pattern of these isolates was studied by disk diffusion Method. RESULTS: Among all 705 stool samples, 36 (5.1%) yielded Shigella. Of cases, 392 (55.6%) were girl and 313 (44.4%) were boy. The most common Shigella isolates were S. flexneri (n=19, 52.7%) followed by S. sonnei (n=11, 30.5%), S. boydii (n=4, 11.1%) and S. dysenteriae 2(5.5%). Of the Shigella isolates, 47.2% showed resistance to two or more antimicrobial agents. Resistance pattern against various antimicrobials were as follows: trimethoprim-sulphamethoxazole (80.5%), ampicillin (63.8%), tetracycline (58.3%), chloramphenicol (33.3%), nalidixic acid (27.7%), and cefixime (16.6%). There was no resistance against ciprofloxacin and ceftriaxone. CONCLUSION: The most common isolates were S. flexneri followed by S. Sonnei. There was no antibiotic resistance against ciprofloxacin and ceftriaxone. TMP-SMZ showed highest resistance pattern.

Neonatal bacteriemia isolates and their antibiotic resistance pattern in neonatal insensitive care unit (NICU) at Beasat Hospital, Sanandaj, Iran.

Bacteremia continues to result in significant morbidity and mortality, particularly among neonates. There is scarce data on neonatal bacteremia in among Iranian neonates. In this study, we determined neonatal bacteremia isolates and their antibiotic resistance pattern in neonatal insensitive care unit at Beasat hospital, Sanandaj, Iran. During one year, all neonates admitted to the NICU were evaluated. Staphylococcal isolates were subjected to determine the prevalence of MRS and mecA gene. A total of 355 blood cultures from suspected cases of sepsis were processed, of which 27 (7.6%) were positive for bacterial growth. Of the 27 isolates, 20 (74%) were Staphylococcus spp as the leading cause of bacteremia. The incidence of Gram negative bacteria was 04 (14.8%). The isolated bacteria were resistant to commonly used antibiotics. Maximum resistance among Staphylococcus spp was against Penicillin, and Ampicillin. In our study, the isolated bacteria were 7.5 % Vancomycin and Ciprofloxacin sensitive. Oxacillin disk diffusion and PCR screened 35% and 30% mec a positive Staphylococcus spp. The spectrum of neonatal bacteremia as seen in NICU at Beasat hospital confirmed the importance of pathogens such as Staphylococcus spp. Penicillin, Ampicillin and Cotrimoxazol resistance was high in theses isolates with high mecA gene carriage, probably due to antibiotic selection.

Candida non albicans with a High amphotericin B resistance pattern causing candidemia among cancer patients.

BACKGROUND: Many scientists have reported Candida species to be of great concern because of the high frequency that they colonize and infect human hosts, particularly cancer patients. Moreover, in the last decades Candida species have developed resistance to many antifungal agents. Based on this, we aimed to identify and determine the prevalence of Candida spp from blood culture bottles among cancer patients and their antifungal resistance pattern. MATERIALS AND METHODS: From the blood culture bottles isolation and identification of the Candida spp were performed by conventional microbiological techniques. The in vitro antibiotic resistance pattern of the isolates was determined by CLSI guidelines. Genomic DNA was isolated and amplified. Each gene was separated by agar gel electrophoresis. RESULTS: Identification of Candida spp was based on the presence of yeast cells in direct examination, culture and DNA extraction. Of the 68 blood samples collected during the study period (April 2013 to October 2013), five (7.35%) were positive for the presence of Candida spp, 2 (40%) of which were identified as Candida albicans and 3 (60%) were Candida non-albicans. CONCLUSIONS: High resistance to amphotricin B was observed among all the Candida non-albicans isolates. Regular investigations into antifungal resistance will help us to get an updated knowledge about their antibiotic resistance pattern which may help the physician in selecting the antibiotics for empirical therapy.

Molecular characterization of class 1 integrons and gene cassettes in multidrug resistant (MDR) Klebsiella spp. isolated from hospitalized and outpatients in Iran, 2009.

BACKGROUND AND OBJECTIVES: Klebsiella species are of the most common bacteria involved in nosocomial and urinary tract infections. Genetic elements such as class 1 integrons have an important role in the resistance development. In this study, the share of class 1 integrons, the genetic characterization of the integron cassettes and PFGE profiles of the clinical Klebsiella isolates are evaluated in Besat University hospital of Sanandaj, Iran. METHODS: Isolates from 17890 clinical specimens were identified by API20E. Antibiotic susceptibility testing and MIC were done for MDR isolates. For investigating class 1 integrons and gene cassettes, PCR by intI1 integrase and 5'-CS/3'-CS were performed. Integrated gene cassettes were analyzed by PCR-RFLP and sequencing. Pulsed-Field Gel Electrophoresis was carried out for studying of clonality outbreak of isolates. RESULTS: Thirty five Klebsiella spp. were isolated and included 29 K. pneumoniae and 6 K. oxytoca. All the isolates were susceptible to carbapenems while other antibiotics showed high resistant profile. In all Klebsiella spp. PCR for intI1 integrase and 5'-CS/3'-CS were positive (100%). Sequencing for prevalent bands of internal variable regions between 5'-CS/3'-CS showed arr-5, orfD-aacA4 and aad5- dfrA17. PFGE Analysis showed 18 clusters in K. pneumoniae with clonality relatedness in some cases but no relatedness among K. oxytoca isolates. CONCLUSION: High prevalence of class 1 integron carrying gene cassettes confirms that integron-mediated antimicrobial gene cassettes are important in Klebsiella spp. resistance profile. Clone diffusions of MDR Klebsiella spp. which harbor class 1 integrons have threaten the potential in the resistance development in our clinical settings.

The prevalence of methicillin resistant Staphylococcus aureus (MRSA) isolates with high-level mupirocin resistance from patients and personnel in a burn center.

The rate of the MRSA strains, particularly at burn centers, is increasing worldwide. Detection of mupirocin resistance MRSA strains in the burn centers particularly from personnel will help to control these strains. For this purpose, a total of 116 Staphylococcus aureus isolates from the patients (burns) and personnel (nostrils) in Ahvaz Taleghani hospital (Iran) were investigated. The methicillin and mupirocin resistant isolates were detected by multiplex amplification of the mecA and ileS-2 genes. The mecA was found among 80% of isolates. The rates of mupirocin resistant strains among personnel and patients were 70% and 6%, respectively. The carriage rates of the S. aureus, MRSA and MRSA with high-level mupirocin resistance in the personnel were 40%, 34% and 28%, respectively. In conclusions, the high prevalence of MRSA strains in the patients showed the potential outbreak of the MRSA in the burn center and highlighted the need of antibiotic susceptibility monitoring of MRSA. Moreover being personnel as a main reservoir in terms of MRSA strains with high-level mupirocin resistance emphasizes the screening of the personnel in terms of the MRSA in the healthcare system especially in the burn center.

First Survey of Metallo-ß-Lactamase Producers in Clinical Isolates of Pseudomonas aeruginosa From a Referral Burn Center in Kurdistan Province.

BACKGROUND: Treatment of infectious diseases is becoming more challenging with each passing year. This is especially true for infections caused by Pseudomonas aeruginosa, an opportunistic pathogen with the ability to rapidly develop resistance to multiple classes of antibiotics. OBJECTIVES: This study was conducted to determine the prevalence of metallo-ß-lactamase (MBL)-producing strains among multidrug-resistant P. aeruginosa strains isolated from burn patients. MATERIALS AND METHODS: The isolates were identified, tested for susceptibility to various antimicrobial agents, and screened for the presence of MßLs by using the double-disk synergy test. The minimal inhibitory concentration of imipenem was determined by microplate broth dilution method on Mueller-Hinton agar. To detect VIM, SIM, and GIM MBLs, the isolates were subjected to polymerase chain reaction. RESULTS: In this study, we identified 100 P. aeruginosa isolates from 176 clinical specimens obtained from burn patients. The isolates showed maximum resistance to ampicillin (100%), ceftazidime (94%), and ceftriaxone (89%). The CLSI-MBL phenotypic test showed that of the 100 P. aeruginosa isolates, 22 (22%) were positive for MBL production in the double-disk synergy test. Of the 22 MBL-positive P. aeruginosa isolates, 8 were resistant to imipenem. PCR analysis showed that 8 isolates were positive for blaVIM1. The other genes blaSIM1 and blaGIM1 were not detected. CONCLUSIONS: The study results demonstrate the serious therapeutic threat of the spread of MBL producers among P. aeruginosa populations. Metallo-ß-lactamases were detected in 22% of imipenem-resistant P. aeruginosa isolates. Early detection and infection-control practices are the best antimicrobial strategies for this organism; therefore, systematic surveillance to detect MBL producers is necessary.