Investigation of the effects of different substrates on the promotion of the soil microbial consortium, encompassing bacteria and fungi, in the bioremediation of decabromodiphenyl ether (BDE-209)

Decabromodiphenyl ether (BDE-209) is recognized as an emerging and hazardous pollutant in numerous ecosystems. Despite this, only a few studies have concurrently investigated the biodegradation of BDE-209 by a microbial consortium comprising both bacteria and fungi. Consequently, the interactions between bacterial and fungal populations and their mutual effects on BDE-209 degradation remain unclear. Our main objective was to concurrently assess the changes and activity of bacterial and fungal communities during the biodegradation of BDE-209 in a real soil matrix. In the present study, various organic substrates were employed to promote soil biomass for the biodegradation of BDE-209. Soil respiration and molecular analysis were utilized to monitor biological activity and biomass community structure, respectively. The findings revealed that the use of wheat straw in the soil matrix resulted in the highest soil respiration and microbial activity among the treatments. This approach obviously provided suitable habitats for the soil microflora, which led to a significant increase in the biodegradability of BDE-209 (49%). Biomass survival efforts and the metabolic pathway of lignin degradation through co-metabolism contributed to the biodegradation of BDE-209. Microbial community analysis identified Proteobacteria (Alphaproteobacteria-Betaproteobacteria), Firmicutes, Bacteroides (bacterial phyla), as well as Ascomycota and Basidiomycota (fungal phyla) as the key microorganisms in the biological community involved in the biodegradation of BDE-209. This study demonstrated that applying wheat straw can improve both the biological activity and the biodegradation of BDE-209 in the soil of polluted sites.

Investigation of antimicrobial resistance patterns and molecular typing of Pseudomonas aeruginosa isolates among Coronavirus disease-19 patients

BACKGROUND

Pseudomonas aeruginosa is a common co-infecting pathogen recognized among COVID-19 patients. We aimed to investigate the antimicrobial resistance patterns and molecular typing of Pseudomonas aeruginosa isolates among Coronavirus disease-19 patients.

METHODS

Between December 2020 and July 2021, 15 Pseudomonas aeruginosa were isolated from COVID-19 patients in the intensive care unit at Sina Hospital in Hamadan, west of Iran. The antimicrobial resistance of the isolates was determined by disk diffusion and broth microdilution methods. The double-disk synergy method, Modified Hodge test, and polymerase chain reaction were utilized to detect Pseudomonas aeruginosa extended spectrum beta-lactamase and carbapenemase producers. Microtiter plate assay was performed to evaluate the biofilm formation ability of the isolates. The isolates phylogenetic relatedness was revealed using the multilocus variable-number tandem-repeat analysis method.

RESULTS

The results showed Pseudomonas aeruginosa isolates had the most elevated resistance to imipenem (93.3%), trimethoprim-sulfamethoxazole (93.3%), ceftriaxone (80%), ceftazidime (80%), gentamicin (60%), levofloxacin (60%), ciprofloxacin (60%), and cefepime (60%). In the broth microdilution method, 100%, 100%, 20%, and 13.3% of isolates showed resistance to imipenem, meropenem, polymyxin B, and colistin, respectively. Ten (66.6%) isolates were identified as multiple drug resistance. Carbapenemase enzymes and extended spectrum beta-lactamases were identified in 66.6% and 20% of the isolates, respectively and the biofilm formation was detected in 100% of the isolates. The blaOXA-48, blaTEM, blaIMP, blaSPM, blaPER, blaVEB, blaNDM, blaSHV, and blaCTX-M genes were detected in 100%, 86.6%, 86.6%, 40%, 20%, 20%, 13.3%, 6.6%, and 6.6% of the isolates, respectively. The blaVIM, blaGIM, blaGES, and blaMCR-1 genes were not identified in any of the isolates. The MLVA typing technique showed 11 types and seven main clusters and most isolates belong to cluster I, V and VII.

CONCLUSION

Due to the high rate of antimicrobial resistance, as well as the genetic diversity of Pseudomonas aeruginosa isolates from COVID-19 patients, it is indispensable to monitor the antimicrobial resistance pattern and epidemiology of the isolates on a regular basis.

Prevalence of Helicobacter felis and Helicobacter heilmannii and Co-infection With Helicobacter pylori in Gastric Biopsy Specimens in Endoscopy Ward of Shahid Beheshti Hospital, Hamadan City, Iran

Background: Helicobacter pylori (H. pylori) has various strains associated with human infections. H. pylori, H. heilmannii, and H. felis are the most common strains in humans. H. pylori is associated with several human diseases such as chronic gastritis, peptic ulcer, mucous membrane lymphoma, and gastric adenocarcinoma. This study aimed to determine the prevalence rates of H. felis and H. heilmannii and the effect of co-infection with H. pylori in gastric biopsy specimens of patients. Methods: Totally, 80 gastric biopsy specimens were taken by a physician from the patients referred to Shahid Beheshti Hospital, Hamadan City, Iran. PCR test was used to confirm the presence of H. pylori in samples that had positive rapid urease tests. Moreover, the ureB gene and ureA and ureB genes were used for H. heilmannii and H. felis, respectively. Results: Of the study patients, 61.5% were females, and 38.5% were males with a mean age of 37.8 years. Of 80 biopsies, 50% were H. pylori-positive, 53.8% were H. heilmannii-positive, but no H. felis was identified in any sample. Results indicate that smoking, having a history of gastrointestinal diseases, and taking certain medications can be risk factors for H. pylori. Conclusion: Any agent contributing to gastric mucosal damage can enhance the susceptibility to bacterial contamination. Overall, the results indicate a low probability of interactions between H. pylori, H. heilmannii, and H. felis.

Prevalence of Helicobacter felis and Helicobacter heilmannii and Co-infection With Helicobacter pylori in Gastric Biopsy Specimens in Endoscopy Ward of Shahid Beheshti Hospital, Hamadan City, Iran

Background: Helicobacter pylori (H. pylori) has various strains associated with human infections. H. pylori, H. heilmannii, and H. felis are the most common strains in humans. H. pylori is associated with several human diseases such as chronic gastritis, peptic ulcer, mucous membrane lymphoma, and gastric adenocarcinoma. This study aimed to determine the prevalence rates of H. felis and H. heilmannii and the effect of co-infection with H. pylori in gastric biopsy specimens of patients. Methods: Totally, 80 gastric biopsy specimens were taken by a physician from the patients referred to Shahid Beheshti Hospital, Hamadan City, Iran. PCR test was used to confirm the presence of H. pylori in samples that had positive rapid urease tests. Moreover, the ureB gene and ureA and ureB genes were used for H. heilmannii and H. felis, respectively. Results: Of the study patients, 61.5% were females, and 38.5% were males with a mean age of 37.8 years. Of 80 biopsies, 50% were H. pylori-positive, 53.8% were H. heilmannii-positive, but no H. felis was identified in any sample. Results indicate that smoking, having a history of gastrointestinal diseases, and taking certain medications can be risk factors for H. pylori. Conclusion: Any agent contributing to gastric mucosal damage can enhance the susceptibility to bacterial contamination. Overall, the results indicate a low probability of interactions between H. pylori, H. heilmannii, and H. felis.

Current Status and Structure Activity Relationship of Privileged Azoles as Antifungal Agents (2016-2020)

Fungal infections have major contribution to the infectious related deaths in recent century. The issue has gotten worse with the advent of immunity impairing conditions such as HIV epidemic. Eukaryote nature of fungal pathogens leads to harder eradication than bacterial infections. Given the importance of the problem, considerable efforts have been put on the synthesis and biological assessment of azole-based chemical scaffolds and their bioisosteres. The emergence of validated macromolecular targets within different fungal species inspires structure-based drug design strategies toward diverse azole-based agents. Despite of advantageous features, emergence of drug-resistant fungal species restrict the applicability of current azoles as the first-line antifungal agents. Consequently, it appears advisable to elucidate SARs and chemical biodiversity within antifungal azoles. Current contribution was devoted to a brief look at clinically applied drugs, structure-based classification of azole antifungals and their structure activity relationships (SARs). Reviewed molecules belong to the antifungal structures that were reported throughout 2016-2020.

The silent presence of Mycoplasma hominis in patients with prostate cancer

BACKGROUND

Mycoplasma hominis, an opportunistic pathogen in human genitourinary tract, can cause chronic infection in the prostate. Intracellular survival of M. hominis leads to a prolonged presence in the host cells that can affect the cell's biological cycle. In the present study, we aimed to evaluate the frequency of M. hominis DNA in prostate tissue of Iranian patients with prostate cancer (PCa) in comparison to a control group with benign prostatic hyperplasia (BPH).

METHODS

This research was a retrospective case-control study using 61 archived formalin-fixed paraffin-embedded (FFPE) blocks of prostate tissue from patients with PCa and 70 FFPE blocks of patients with BPH. Real-time PCR, targeting two different genes, 16S rRNA and yidC, in the M. hominis genome was performed for all specimens.

RESULTS

Out of 61 blocks of prostate biopsy from patients with PCa, eight samples (13%) were positive for M. hominis, while the bacterium was not detected in any of the 70 blocks of patients with BPH (P value, 0.002).

CONCLUSIONS

The high frequency of M. hominis in patients with PCa likely shows a hidden role of the organism in prostate cancer during its chronic, apparently silent and asymptomatic colonization in prostate.

Prevalence and Expression of Genes of Type II Antitoxin Toxin Systems in Clinical Isolates of Methicillin-Resistant Staphylococcus aureus

Objectives: Antibiotic resistance of bacteria has been increasing in recent years and reports indicate that some bacterial strains are even resistant to the last treatment line. The survey of MazEF antitoxin-toxin genes in 84 strain of MRSA and and the antimicrobial effect of supernatants on the logarithmic growth stage of the bacteria. Methods: In this study, 84 strains of MRSA were collected. The patients included 48 males and 36 females with a mean age of 39 years.  The primers for Staphylococcus aureus type II antitoxin genes were designed. In the first step, using the mecA primer and PCR, the strains were genetically examined to confirm methicillin-resistant Staphylococcus aureus. In the next step, the frequency of MazEF antitoxin-toxin genes was examined. Results: All strains of methicillin-resistant Staphylococcus aureus had the F maz gene except one. The highest antibiotic resistance was related to the strains isolated from the wound and the lowest resistance was related to the strains isolated from the urine. the effect of the supernatant obtained in the death phase of Staphylococcus aureus was assessed and the antimicrobial effect of these supernatants on the logarithmic growth stage of the bacteria was measured. Conclusion: since previous studies showed the antimicrobial effect of this supernatant on many other bacteria, a type II system was suspected that was confirmed by the results.

Molecular typing, biofilm production, and detection of carbapenemase genes in multidrug-resistant Acinetobacter baumannii isolated from different infection sites using ERIC-PCR in Hamadan, west of Iran

BACKGROUND

Acinetobacter baumannii is an opportunistic pathogen that can cause several kinds of nosocomial infections. Increasing antibiotic resistance as well as identifying genetic diversity and factors associated with pathogenicity and prevalence of this bacterium is important. The aim of this study was the investigation of molecular typing, biofilm production, and detection of carbapenemase genes in multidrug-resistant Acinetobacter baumannii isolated from different infection sites using ERIC-PCR in Iran.

METHODS

Forty isolates of A. baumannii were obtained from various wards of the central hospital, in the west of Iran. Phenotypic identification and genetic diversity, biofilm production assay, and detection of Carbapenemase genes carried out.

RESULTS

Tracheal samples 26 (61.9 %) are the most frequent isolates, and 95 % of isolates were identified as MDR. 32.5 % of all A. baumannii strains were capable to form a strong biofilm. It was founded that antimicrobial resistance patterns had a significant relationship with strong biofilm formation (P = 0.001). Most frequencies of the studied genes were in the order of VIM (81 %), SPM (45.2 %), and IMP (35.7 %) genes. The VIM gene was the most frequent in all isolates which were significant (P = 0.006). 14 different ERIC-types were observed including 7 common types and 7 unique or single types. F type is the largest common type consisting of nine isolates and B, D, and E types contain two isolates separately.

CONCLUSIONS

ERIC-PCR technique was used to genetically classify A. baumannii isolates as one of the most common microorganisms in nosocomial infections.

An update on prevalence of slow-growing mycobacteria and rapid-growing mycobacteria retrieved from hospital water sources in Iran - a systematic review

Introduction

This study aimed to assess the prevalence of slow growing mycobacteria (SGM) and rapid-growing mycobacteria (RGM) retrieved from hospital water sources in Iran from 2016 to 2020.

Methods

The review was conducted to get eligible published studies from 1^st January 2016 to 25^th March 2020 based on PRISMA protocol. A combination of related words from the Medical Subject Heading Terms (MeSH), with (AND, OR) were used to search for published studies reporting the prevalence of nontuberculous mycobacteria (NTM) in Scopus, MEDLINE, Web of Sciences, Google Scholar, and Iranian databases. Then data from the studies were extracted and reported.

Results

Our study showed that different water sources of hospitals were contaminated with NTMs. The prevalence of RGM isolates in hospital water samples varied between 42.2%-67.5%, and the prevalence of SGM varied between 32.5%-57.7%, respectively. M. lentiflavum (84.7%), M. avium complex(2.8%-56.4%)and M. gordonae (2.8%-56.2%) were the most prevalent NTM species amongst SGM, whereas M. fortuitum (2.9%-44.2%), M. chelonae (8%-36.8%), M. mucogenicum (8%-25.6%) were the most leading NTM isolates among RGM.

Conclusions

A high prevalence of NTM was reported from hospital environments particularly hospital water sources which can colonize medical devices, solutions, and water used for patients and cause nosocomial infection. Therefore, the hospitals should check the microbiological quality of the water used.

Prevalence of Common Nosocomial Infections and Evaluation of Antibiotic Resistance Patterns in Patients with Secondary Infections in Hamadan, Iran

Introduction

The prevalence of nosocomial infections in patients hospitalized to three hospitals of Shahid Beheshti, Farshchian, and Be’ saat in Hamadan was investigated for 2 years (2018 to 2020).

Materials and Methods

The samples were cultured and characterized using morphological and diagnostic biochemical tests. The analysis of the frequency of the isolates and their antibiotic resistance were calculated using SPSS (version 22) at a significant level of P-value < 0.05.

Results

Bacterial isolates were collected from the 1194 clinical specimens, of which 1394 were isolated from urine, 16 from CSF, and 588 from tracheal aspiration. Also, 654 (54.8%) isolates were obtained from females and 540 (45.2%) from males with the age range 15–73 years (P> 0.05). The results showed that 22.1% were gram-positive and 77.9% were gram-negative. In our study, the frequency of Klebsiella pneumoniae bacteria was higher than in some studies, and this indicates the genetic changes and resistance of this bacterium to many antibiotics.

Conclusion

To prevent further spread of resistance, increase the effectiveness of antibiotics and prevent multidrug resistance, it is essential to establish a precise schedule for the use of antibiotics and assess the resistance pattern periodically in each region based on the antibiotic resistance pattern.

Detection of Virulence Factors and Antibiotic Resistance Pattern of Clinical and Intensive Care Unit Environmental Isolates of Pseudomonas aeruginosa

BACKGROUND

Pseudomonas aeruginosa is a gram-negative non-glucose fermenting aerobic bacteria and an opportunistic pathogen in humans and animals. The present study was carried out to investigate the distribution of virulence factors and antibiotic resistance properties of P. aeruginosa isolated from patients and intensive care unit (ICU) environment.

MATERIAL AND METHODS

A total of 116 P. aeruginosa isolated from patients and ICU environment were collected from Besat hospital in Hamadan, the West of Iran. P. aeruginosa isolates were analyzed based on the presence of the virulence factors encoding genes included exoA, exoS, exoU, and algD using polymerase chain reaction (PCR). Antimicrobial susceptibility test was performed using a disk diffusion method.

RESULTS

The results showed the prevalence of exoA 33 (56.9%), exoS 21 (36.20%), exoU 37 (63.8%), and algD 35 (60.34%) genes in ICU environment P. aeruginosa strains and exo A 23 (39.25%), exoS 25 (43.1%), exoU 40(68.98%), and algD 25 (43.1%) genes in clinical isolates of P. aeruginosa. High resistance levels of the clinical and ICU environment isolate to ampicillinsulbactam (100%), were also observed.

CONCLUSION

Our findings should raise awareness about antibiotic resistance in hospitalized patients in Iran. Clinicians should exercise caution in prescribing antibiotics, especially in cases of human infections.

Evaluation of the prevalence of Legionella pneumophila in Iranian clinical samples: A systematic review and meta-analysis

BACKGROUND

Legionella pneumophila is the main cause for community-acquired pneumonia especially in hospital environments. In this systematic review and meta-analysis, we evaluated the prevalence of L. pneumophila in clinical samples obtained from Iranian patients.

METHODS

The studies reporting L. pneumophila prevalence in Iranian clinical samples that were published between January 2000 and July 2016 were recruited. Comprehensive Meta-Analysis Software (version 3.3.070) was used for quantitative data analysis. Because of high heterogeneity between the studies according to the Cochrane Q and I² statistics, a random-effects model was used for meta-analysis.

RESULTS

Sixteen studies encompassing 1956 subjects were included in the meta-analysis. The overall prevalence of L. pneumophila was 9.6% in clinical samples obtained from the Iranian patients. The age spectrum ranged from 6 months to 80 years old. Dyspnea and cough comprised the most common clinical manifestations. In the subgroup analysis, the prevalence of L. pneumophila was higher in studies with sample size ≤100 (12.9%) in comparison with studies with sample size >100 (8.4%). In addition, the prevalence of L. pneumophila was higher in the years 2009-2016 (9.2%) compared with 2000-2008 (0.7%).

CONCLUSION

L. pneumophila is a major cause of community- and hospital-acquired pneumonia. It is of pivotal importance to implement sensitive and reliable molecular and culture-based techniques to detect and control this infection in healthcare environments.

Diversity of aminoglycoside modifying enzymes and 16S rRNA methylases in Acinetobacter baumannii and Acinetobacter nosocomialis species in Iran; wide distribution of aadA1 and armA

PURPOSE

Acinetobacter baumannii-calcoaceticus complex (ABC) make a great burden on health-care systems due to hospital-acquired infections and antibacterial resistance. Aminoglycoside in combination with other antibacterials used as treatment options. However, ABC species overcome this class of antibacterials in different ways. This study provides a comprehensive report on the distribution of aminoglycoside modifying enzymes (AMEs) and 16S rRNA methylase in Acinetobacter baumannii and Acinetobacter nosocomialis isolated from various provinces in Iran.

METHODS

During six month of study, from eight referral centers in seven provinces across the country, Iran, 178 A. baumannii and 43 A. nosocomialis isolates were collected. The minimum inhibitory concentration of amikacin, gentamicin, netilmicin, kanamycin and tobramycin were measured by microbroth dilution method. AMEs and 16S rRNA methylase variants were sought by PCR.

RESULTS

High rates of resistance were seen in all centers. MIC₅₀ and MIC₉₀ for all A. baumannii and A. nosocomialis isolates from different centers were > 512 mg/L. The most frequent AME was ant(3″)-Ia (aadA1) in both of A. baumannii (74.1%) and A. nosocomialis (86%). armA was detected in A. baumannii and A. nosocomialis at the frequency of 41.6% and 67.4%, respectively. rmtA, B, C, D, aac(3)-Ia (aacC1) and aac(6')-Im were not detected, neither in A. baumannii nor A. nosocomialis. Moreover, aac(6')-Ih was only found in A. baumannii isolates. The distribution of some of the ARGs was limited to a definite center.

CONCLUSION

The overall high-level carriage of ARGs in Acinetobacter species may limited usage of this class of antibacterials as a treatment option.

Molecular characterization of clinical and environmental Pseudomonas aeruginosa isolated in a burn center

In burn centers, Pseudomonas aeruginosa acts as a major cause of nosocomial infections. Therefore, this study aimed to characterize molecularly P. aeruginosa isolates collected from environmental samples and burn patients. A total of 78 strains (including 58 clinical and 20 environmental isolates) of the P. aeruginosa were collected from Beasat hospital of Hamadan, west of Iran, and was identified using API 20NE. The disk diffusion method according to the CLSI was applied for determination of the antimicrobial resistance. Moreover, the microtiter plate test was used for the quantification of Biofilm formation. The genomic features of the isolated strains was evaluated using Pulsed Field Gel Electrophoresis (PFGE). We found that 94.8% of clinical and 80% environmental isolates were capable of forming biofilm. The rate of MDR in clinical and environmental isolates was 51.7% and 40%, respectively. A significant relationship was observed between biofilm formation capability and multiple drug resistance (p < 0.05). PFGE typing showed 11 different clusters with two major clusters A with 30 (38.5%) and B with 14 (17.9%) members, containing up to 56.4% of all isolates. There was no relationship between biofilm formation ability and antibiotic resistance patterns with PFGE patterns. According to the results, the clonal spread of environmental P. aeruginosa isolates is associated with clinical isolates, and both environmental and clinical isolates are attributed to a high prevalence of the antibiotic resistance and biofilm formation ability. This study highlighted that the prevention programs should be implemented in the hospital environment to control the spread of P. aeruginosa in burn units.

Comparison of ultrasonic with stirrer performance for removal of sunset yellow (SY) by activated carbon prepared from wood of orange tree: artificial neural network modeling

The present work focused on the removal of sunset yellow (SY) dye from aqueous solution by ultrasound-assisted adsorption and stirrer by activated carbon prepared from wood of an orange tree. Also, the artificial neural network (ANN) model was used for predicting removal (%) of SY dye based on experimental data. In this study a green approach was described for the synthesis of activated carbon prepared from wood of an orange tree and usability of it for the removal of sunset yellow. This material was characterized using scanning electron microscopy (SEM) and transmission electron microscopy (TEM). The impact of variables, including initial dye concentration (mg/L), pH, adsorbent dosage (g), sonication time (min) and temperature (°C) on SY removal were studied. Fitting the experimental equilibrium data of different isotherm models such as Langmuir, Freundlich, Temkin and Dubinin-Radushkevich models display the suitability and applicability of the Langmuir model. Analysis of experimental adsorption data by different kinetic models including pseudo-first and second order, Elovich and intraparticle diffusion models indicate the applicability of the second-order equation model. The adsorbent (0.5g) is applicable for successful removal of SY (>98%) in short time (10min) under ultrasound condition.

An ultra-sensitive impedimetric immunosensor for detection of the serum oncomarker CA-125 in ovarian cancer patients

Effective treatment of ovarian cancer depends upon the early detection of the malignancy. Here, we report on the development of a new nanostructured immunosensor for early detection of cancer antigen 125 (CA-125). A gold electrode was modified with mercaptopropionic acid (MPA), and then consecutively conjugated with silica coated gold nanoparticles (AuNP@SiO2), CdSe quantum dots (QDs) and anti-CA-125 monoclonal antibody (mAb). The engineered MPA|AuNP@SiO2|QD|mAb immunosensor was characterised using transmission electron microscopy (TEM), atomic force microscopy (AFM), cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS). Successive conjugation of AuNP@SiO2, CdSe QD and anti-CA-125 mAb onto the gold electrode resulted in sensitive detection of CA-125 with a limit of detection (LOD) of 0.0016 U mL(-1) and a linear detection range (LDR) of 0-0.1 U mL(-1). Based on the high sensitivity and specificity of the immunosensor, we propose this highly stable and reproducible biosensor for the early detection of CA-125.