Green synthesis and characterization of α-Mn2O3 nanoparticles for antibacterial activity and efficient visible-light photocatalysis.

In this study, green synthesis, characterizations, photocatalytic performance, and antibacterial applications of α-Mn2O3 nanoparticles are reported. The synthesized nanoparticles were characterized by Fourier transform infrared spectroscopy (FT-IR), powder X-ray diffraction (XRD), transmission electron microscope (TEM), Scanning electron microscopy (SEM), energy dispersive X-ray analysis (EDX), Brunauer Emmett Teller (BET), Electrochemical Impedance Spectroscopy (EIS), Photoluminescence (PL), and Differential reflectance spectroscopy (DRS) analysis. The investigation verified that the α-Mn2O3 nanoparticles possessed a cubic structure, with a crystallite size of 23 nm. The SEM and TEM techniques were used to study the nanoscale morphology of α- Mn2O3 nanoparticles, which were found to be spherical with a size of 30 nm. Moreover, the surface area was obtained as 149.9 m2 g-1 utilizing BET analysis, and the band gap was determined to be 1.98 eV by DRS analysis. The photocatalysis performance of the α-Mn2O3 NPs was evaluated for degrading Eriochrome Black T (EBT) dye under visible light and degradation efficiency was 96% in 90 min. The photodegradation mechanism of EBT dye was clarified with the use of radical scavenger agents, and the degradation pathway was confirmed through Liquid Chromatography-Mass Spectrometry (LC-MS) analysis. Additionally, the produced nanoparticles could be extracted from the solution and continued to exhibit photocatalysis even after five repeated runs under the same optimal conditions. Also, the antibacterial activity of green synthesized α-Mn2O3 nanoparticles was investigated by using the broth microdilution method towards Enterococcus faecalis ATCC 29212 (Gram-positive), Staphylococcus aureus ATCC 29213 (Gram-positive), Salmonella typhimurium ATCC 14028 (Gram-negative), Klebsiella pneumoniae ATCC 7881 (Gram-negative), Escherichia coli ATCC 25922 (Gram-negative), Proteus mirabilis ATCC 7002 (Gram-negative), and Pseudomonas aeruginosa ATCC 27853 (Gram-negative) bacterial strains.

Systematic review and meta-analysis of the global prevalence of sexually transmitted infections in people living with HIV and associated risk factors.

People living with HIV (PLWH) constitute a vulnerable population for acquiring additional sexually transmitted infections (STIs). This study was conducted to provide a summary of the evidence on the global prevalence of STIs in PLWH with an emphasis on infectious agents, diagnostic methods, and related risk factors. PubMed, Scopus, and Web of Science were systematically searched to include records published from January 01, 1990, to January 31, 2022, and the Google Scholar search engine was used to check the search strategy. In total, 132 eligible studies reporting STIs in PLWH were included, enrolling subjects from 35 countries across five continents. The pooled proportion of STIs was estimated to be 30.23% (95% CI, 26.1-34.45%) in PLWH and 20.01% (95% CI, 17.17-23.01%) in HIV-negative patients. Our meta-analysis indicated that in PLWH, the pooled OR of STIs compared to HIV-negatives was 1.77 (95% CI: 1.58-1.98) (p < 0.0001). The pooled OR of STIs by viral infectious agents was highest in PLWH (52.19% [95% CI: 43.88-60.43]) compared with fungal (22.19% [95% CI: 15.64-29.53]), bacterial (19.07% [95% CI: 13.59-26.63]), and parasitic (14.05% [95% CI: 11.88-16.38]) infections. Our findings show that there is a rather significant frequency of STIs among PLWH. This study highlights the need for new programs for the detection, treatment, and prevention of STIs in this at-risk population.

Prevalence, Antibiotic Resistance and Virulence of Enterococcus spp. Isolated from Traditional Cheese Types.

Background: Enterococci are naturally found in the gastrointestinal (GI) tract of animals and humans, as well as animal-derived foods and vegetables. We here aimed to determine the prevalence, antibiotic resistance, and virulence determinants of E. faecium and E. faecalis in traditional cheese in the North-west of Iran. Materials and Methods: Fifty specimens of popular traditional cheese from dairy stores of Urmia and Tabriz, Iran, were collected. Identification of the genus and species of enterococci was done using molecular and phenotypic techniques. Results: Forty-eight (96 %) of 50 traditional cheese samples were harboring Enterococcus spp, including Enterococcus faecalis (n= 40; 83.33 %) and E. faecium (n= 8; 16.67 %). The prevalence of enterococci ranged from 1.1×105 to 9.7×104 CFU/g, and 1.1×103 to 9.8×103 CFU/g in Urmia and Tabriz samples, respectively. Rifampicin resistance (n= 38; 79.2 %) was the most common pattern observed in the susceptibility test, which was followed by quinupristin/dalfopristin (n= 33; 68.75 %). Among E. faecalis isolates, cpd (100 %), ace (92.5 %) and gelE (87.5 %), and among E. faecium isolates, gelE (100 %) and asa1 (75 %) were found to have the most common virulence genes. Conclusion: E. faecalis was the predominant species, displaying more virulence determinants. It also had high antibiotic resistance, as compared to E. faecium. The enterococci identified here commonly expressed virulence and antibiotic resistance determinants. So, it is required to improve the maintenance and production quality of traditional cheese to avoid enterococci contamination.

The effect of bacterial composition shifts in the oral microbiota on Alzheimer's disease.

Alzheimer's disease (AD), a neurological disorder, despite significant advances in medical science, has not yet been definitively cured, and the exact causes of the disease remain unclear. Due to the importance of AD in the clinic, large expenses are spent annually to deal with this neurological disorder, and neurologists warn of an alarm to increase this disease in the elderly people in the near future. It has been believed that microbiota dysbiosis lead to Alzheimer's as a multi-step disease. In this regard, the presence of footprints of perturbations in the oral microbiome and the predominance of pathogenic bacteria and their effect on the nervous system especially AD is a very interesting topic that has been considered by researchers in the last decade. Some studies have looked at the mechanisms by which oral microbiota cause AD. However, many aspects of this interaction are still unclear as to how oral microbiota composition can contribute to this disease. Understanding this interaction requires extensive collaboration by interdisciplinary researchers to explore all aspects of the issue. So, in this review has attempted to give the mechanisms of shift of oral microbiota in AD in order to reveals the link between microbiota composition and this disease with the help of researchers from different fields.

Application of next-generation sequencing in the diagnosis of gastric cancer.

Objectives: Gastric cancer (GC) is a disease with high mortality, poor prognosis and numerous risk factors. GC has an asymptomatic nature in early stages of the diseases, making timely diagnosis complicated using common conventional approaches, namely pathological examinations and imaging tests. Recently, molecular profiling of GC using next generation sequencing (NGS) has opened new doors to efficient prognostic, diagnostic, and therapeutic strategies. The current review aims to thoroughly discuss and compare the current NGS techniques and commercial platforms utilized for GC diagnosis and treatment, highlighting the most recent NGS-based GC studies. Furthermore, this review addresses the challenges of clinical implementation of NGS in GC.Materials and methods: This review was conducted according to the eligible studies identified via search of Web of Science, PubMed, Scopus, Embase and the Cochrane Library. In the present study, data on gastric cancer patients and NGS methods used to diagnose the disease were reviewed.Conclusion: Given the ever-rising advancements in NGS technologies, bioinformatics, healthcare guidelines and refined classifications, it is hoped that these technologies can actualize their advantages and optimize GC patients' experience.

In-silico design of a multi-epitope for developing sero-diagnosis detection of SARS-CoV-2 using spike glycoprotein and nucleocapsid antigens.

COVID-19 is a pandemic disease caused by novel corona virus, SARS-CoV-2, initially originated from China. In response to this serious life-threatening disease, designing and developing more accurate and sensitive tests are crucial. The aim of this study is designing a multi-epitope of spike and nucleocapsid antigens of COVID-19 virus by bioinformatics methods. The sequences of nucleotides obtained from the NCBI Nucleotide Database. Transmembrane structures of proteins were predicted by TMHMM Server and the prediction of signal peptide of proteins was performed by Signal P Server. B-cell epitopes' prediction was performed by the online prediction server of IEDB server. Beta turn structure of linear epitopes was also performed using the IEDB server. Conformational epitope prediction was performed using the CBTOPE and eventually, eight antigenic epitopes with high physicochemical properties were selected, and then, all eight epitopes were blasted using the NCBI website. The analyses revealed that α-helices, extended strands, ß-turns, and random coils were 28.59%, 23.25%, 3.38%, and 44.78% for S protein, 21.24%, 16.71%, 6.92%, and 55.13% for N Protein, respectively. The S and N protein three-dimensional structure was predicted using the prediction I-TASSER server. In the current study, bioinformatics tools were used to design a multi-epitope peptide based on the type of antigen and its physiochemical properties and SVM method (Machine Learning) to design multi-epitopes that have a high avidity against SARS-CoV-2 antibodies to detect infections by COVID-19.

CRISPR-Cas Technology: Emerging Applications in Clinical Microbiology and Infectious Diseases.

Through the years, many promising tools for gene editing have been developed including zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), CRISPR-associated protein 9 (Cas9), and homing endonucleases (HEs). These novel technologies are now leading new scientific advancements and practical applications at an inimitable speed. While most work has been performed in eukaryotes, CRISPR systems also enable tools to understand and engineer bacteria. The increase in the number of multi-drug resistant strains highlights a necessity for more innovative approaches to the diagnosis and treatment of infections. CRISPR has given scientists a glimmer of hope in this area that can provide a novel tool to fight against antimicrobial resistance. This system can provide useful information about the functions of genes and aid us to find potential targets for antimicrobials. This paper discusses the emerging use of CRISPR-Cas systems in the fields of clinical microbiology and infectious diseases with a particular emphasis on future prospects.

Fha Deficient Bordetella pertussis Isolates in Iran with 50 Years Whole Cell Pertussis Vaccination.

BACKGROUND: Bordetella pertussis, a highly contagious respiratory. Notably, the resurgence of pertussis has recently been associated with the lacking production of vaccine virulence factors. This study aimed to screen pertactin (Prn) and filamentous hemagglutinin (Fha) production in Iran with 50 years' whole cell vaccine (WCV) immunization program. METHODS: Overall, 130 B. pertussis isolates collected from Pertussis Reference Laboratory of Iran during 2005-2018. Real-time PCR was performed by targeting IS481, ptxP, IS1001 and IS1002 for species confirmation of B. pertussis. Western-blot was used to evaluate the expression of virulence factors (pertactin and filamentous hemagglutinin). RESULTS: All tested B. pertussis isolates expressed Prn and all except two isolates expressed Fha. We have sequenced genomes of these strains and identified differences compared with genome reference B. pertussis Tohama I. CONCLUSION: Many countries reporting Prn and Fha-deficiency due to acellular vaccine (ACV) pressure. Our results demonstrate in a country with WCV history, Fha-deficient isolates may rise independently. However, Prn-deficient isolates are more under the ACV pressure in B. pertussis isolates. Continues surveillance will provide a better understanding of the effect of WCV on the evolution of the pathogen deficiency.

Right atrial clot and pulmonary embolism in a patient with COVID-19: A case report.

The infection caused by the novel coronavirus (COVID-19) immersed the globe into a widespread pandemic. The disease leads to acute respiratory disease syndrome , hypercoagulation, and cardio-vascular diseases. In this case report, we presented an 80-year-old man with right atrial clot and acute pulmonary embolism, who was diagnosed with COVID-19. The patient was isolated and transferred to the intensive care unit with a diagnosis of submissive pulmonary thromboembolism and right atrial clot following COVID-19 infection. Antibiotics and anticoagulants were administered, and the patient was referred for mechanical thrombectomy. He did not die and after recovery, was discharged with warfarin administration. Preventing thromboembolic events seems to be the first priority in the management of COVID-19 patients. It is necessary to look for strategies to manage and prevent the early occurrence of thromboembolic events in these patients.

Acute upper limb ischemia in a patient with COVID-19: A case report.

The novel pandemic of coronavirus infection (COVID-19) has been linked with coagulopathy and thromboembolic events, causing limb loss and finally death. The present report describes a case of upper limb ischemia in a patient with COVID-19 infection, who lacked conventional risk factors for acute limb ischemia (ALI).mAn 83 year-old man with intraluminal thrombus and the occlusion of the axillary and brachial arteries, ceasing blood supply to the distal part of the body, was tested positive for the COVID-19 infection. The patient received therapeutic anticoagulation and underwent open thromboembolectomy, which failed to save the patient's life. The link between COVID-19 and thromboembolism remains unknown and needs further studies to be disclosed.

Antimicrobial Susceptibility, Serotyping, and Molecular Characterization of Antibiotic Resistance Genes in Listeria monocytogenes Isolated from Pregnant Women with a History of Abortion.

BACKGROUND: Listeria monocytogenes show high mortality among pregnant women and newborns. This study aimed to detect L. monocytogenes in pregnant women with a history of abortion and assess the serotypes, antibiotic susceptibility patterns, and its resistance genes. METHODS: Overall, 400 vaginal swabs were taken from pregnant women with a history of abortion in the past few years in a tertiary care hospital in Tehran, Iran, during 2015-2018. Antibiotics susceptibility to a panel of 10 antibiotics was determined using the standard disk diffusion method and the isolates serotyped by the agglutination method. The antimicrobial-resistant isolates were also screened for the presence of tetM, ermB and dfrD genes by PCR. RESULTS: Overall, 22 L. monocytogenes isolates were identified. High rates of resistance were observed for trimethoprim (50%; n=11), sulphamethoxazole (50%; n=11), tetracycline (45.45%; n=10) and gentamicin (36.36%; n=8). From 22 L. monocytogenes isolates, 13 (59.10 %), 5 (22.73%), 3 (13.63%) and 1 (4.54%) belonged to serotypes 4b, 1/2a, 1/2b, and 3c, respectively. The genetic determinant tetM was detected in 70% of the tetracycline-resistant isolates. Out of 11 trimethoprim-resistant isolates, 27.27% isolates contained dfrD. Moreover, the ermB gene was found in 83.33% of the erythromycin-resistant isolates. CONCLUSION: Ampicillin and partly penicillin consider to be suitable antimicrobial agents to treat human listeriosis. Moreover, due to resistance against many antibiotics, it is necessary to continue monitoring and managing antimicrobial resistance.

Development of a SYBR Green Multiplex Real Time PCR for Simultaneous Detection of Mycobacterium Tuberculosis and Nocardia Asteroides in Respiratory Samples.

BACKGROUND: Nocardia asteroides and Mycobacterium tuberculosis are worldwide-distributed bacteria. These infectious agents can cause many infections in humans, especially in immunocompromised individuals. Pulmonary infections are more common and have similar clinical symptoms. Proper diagnosis and treatment of these patients are important for accurate treatment and could be lifesaving. METHODS: In this study, a multiplex real-time PCR assay was established for the simultaneous detection of the N. asteroides and M. tuberculosis. Both this homemade multiplex real time PCR and routine commercial tuberculosis tests were performed on 150 pulmonary specimens collected from individuals suspected to have tuberculosis. RESULTS: From 150 specimens, 20 samples were acid fast positive, 14 positives for M. tuberculosis by singleplex real time PCR, 10 positives for N. asteroides by singleplex real time PCR and 2 positives for M. tuberculosis and N. asteroides by multiplex real time PCR whereas 14 samples were positive for M. tuberculosis with commercial test. Differential diagnosis of pulmonary tuberculosis is useful for their proper treatment. CONCLUSION: Our test had good performance for differential diagnosis of tuberculosis and nocardiosis. Therefore, it is recommended to be used to diagnose such patients.

First Detection and Characterization of Macrolide-Resistant Mycoplasma pneumoniae from People with Community-Acquired Pneumonia in Iran.

Objectives: Increasing macrolide resistance of Mycoplasma pneumoniae strains is becoming a public health concern worldwide. Nevertheless, no comprehensive genomic background of circulating isolates is available in our region. We aimed to study the genetic diversity of this microorganism using the multiple-locus variable-number tandem-repeat analysis method and to investigate the relationships between MLVA types and macrolide susceptibility profiles of the isolates. Materials and Methods: A total of 270 patients attending Tehran general university hospitals were included in this study. One throat swab was taken from each patient. M. pneumoniae was identified using culture and PCR assay. Macrolide resistance was determined using the broth microdilution method. The MLVA was performed by amplification of four variable-number tandem-repeat loci. Results: Of 270 specimens, M. pneumoniae was detected in 25.2% (n = 68) and 21.8% (n = 59) samples using PCR and culture, respectively. Approximately 56.9% of isolates were resistant to macrolides. Fifty-one of 59 M. pneumoniae isolates were divided into 6 distinct MLVA types. Conclusion: The macrolide-resistant M. pneumoniae (MRMP) rate in this study was relatively high and most of the MRMP isolates were assigned into the type 4/5/7/2. Since a significant association between MLVA type 4/5/7/2 and macrolide resistance of M. pneumoniae isolates was observed, further monitoring of genetic diversity of MRMP isolates might facilitate better understanding of epidemiology of this microorganism. Besides surveillance of the antibiotic susceptibility might be helpful to make necessary reconsiderations on guidelines for treatment of M. pneumoniae infection.

A Meta-Analysis of the Prevalence of Class 1 Integron and Correlation with Antibiotic Resistance in Pseudomonas aeruginosa Recovered from Iranian Burn Patients.

The role of integrons has been highlighted in antibiotic resistance among Pseudomonas aeruginosa isolates. Therefore, we here reviewed the prevalence of class 1 integrons and their correlations with antibiotic resistance of P. aeruginosa isolated from Iranian burn patients. This review was conducted according to the guidelines of Preferred Reporting Items for Systematic Review and Meta-Analyses (PRISMA). Cross-sectional and cohort studies published from January 1, 2000 until December 31, 2018 were enrolled. Meta-analysis was performed by Comprehensive Meta-Analysis (CMA) software using the random effects model, Cochran's Q, and I2 tests. Publication bias was estimated by Funnel plot and Egger's linear regression test. Nine out of 819 studies met the eligibility criteria. The overall combined prevalence of class 1 integrons in P. aeruginosa isolates was 69% (95% confidence interval [CI]: 50.5-83%). The highest combined resistance was reported against Cloxacillin (87.7%), followed by Carbenicillin (79.1%) and Ceftriaxone (77.3%). The combined prevalence of multidrug-resistant (MDR) isolates was 79.3% (95% CI: 31.1-97%). Also, a significant correlation was noted between the presence of class 1 integrons and antibiotic resistance in 55.5% of the included studies (P < .05). The results showed high prevalence of class 1 integrons, antibiotic resistance, and MDR strains in P. aeruginosa isolated from Iranian burn patients. Also, most of the included studies showed a significant correlation between the presence of class 1 integrons and antibiotic resistance.

Fusobacterium nucleatum and colorectal cancer: A mechanistic overview.

Colorectal cancer (CRC) is the third most prevalent cancer in the world. There are many risk factors involved in CRC. According to recent findings, the tumor microenvironment and feces samples of patients with CRC are enriched by Fusobacterium nucleatum. Thus, F. nucleatum is proposed as one of the risk factors in the initiation and progression of CRC. The most important mechanisms of Fusobacterium nucleatum involved in CRC carcinogenesis are immune modulation (such as increasing myeloid-derived suppressor cells and inhibitory receptors of natural killer cells), virulence factors (such as FadA and Fap2), microRNAs (such as miR-21), and bacteria metabolism. The aim of this review was to evaluate the mechanisms underlying the action of F. nucleatum in CRC.

Prevalence, antimicrobial susceptibility, serotyping and virulence genes screening of Listeria monocytogenes strains at a tertiary care hospital in Tehran, Iran.

BACKGROUND AND OBJECTIVES: Listeria monocytogenes is the etiological agent of listeriosis, a highly fatal infection which causes miscarriage or stillbirth in pregnant women. The objective of this study was to detect the prevalence, serotypes, antimicrobial susceptibility and virulence factors of L. monocytogenes isolated from pregnant women with vaginitis at a tertiary care hospital in Tehran, Iran. MATERIALS AND METHODS: During September 2015 to February 2017, a total of 400 vaginal swabs were collected from pregnant women. The presumptive isolates were characterized biochemically. All L. monocytogenes isolates were further analyzed by serotyping and antimicrobial susceptibility tests. All positive samples for L. monocytogenes were analyzed for presence of virulence genes (hlyA, actA, inlA, inlC, inlJ and prfA). RESULTS: Twenty-two (5.5%) of the samples were found positive for presence of L. monocytogenes. Most isolates are resistant to trimethoprim/sulfamethoxazole (81.82%) and chloramphenicol (54.55%). The majority of tested isolates (59.10%) belonged to serotype 4b, followed by 1/2a (22.73%), 1/2b (13.63%), and 3c (4.54%). The hlyA, actA and inlA were detected in all of the 22 L. monocytogenes isolates, but two, three and five isolates were found to lack inlC, inlJ and prfA, respectively. Only one isolate lacked three inlC, inlJ and prfA genes, and two isolates simultaneously lacked both inlJ and prfA genes. CONCLUSION: Evaluation of virulence factors and antimicrobial susceptibility can be highly helpful to develop effective treatment strategies against L. monocytogenes infections. This study is noteworthy in that it documents prevalence, virulence characteristics, and antimicrobial resistance of L. monocytogenes.

Application of Next-generation Sequencing in Clinical Molecular Diagnostics

ABSTRACT Next-generation sequencing (NGS) is the catch all terms that used to explain several different modern sequencing technologies which let us to sequence nucleic acids much more rapidly and cheaply than the formerly used Sanger sequencing, and as such have revolutionized the study of molecular biology and genomics with excellent resolution and accuracy. Over the past years, many academic companies and institutions have continued technological advances to expand NGS applications from research to the clinic. In this review, the performance and technical features of current NGS platforms were described. Furthermore, advances in the applying of NGS technologies towards the progress of clinical molecular diagnostics were emphasized. General advantages and disadvantages of each sequencing system are summarized and compared to guide the selection of NGS platforms for specific research aims.

Pulmonary nocardiosis associated with cerebral abscess successfully treated by co-trimoxazole: a case report.

Nocardiosis is an acute or chronic infectious disease caused by the soil-borne filamentous bacteria belonging to the genus Nocardia. The organisms opportunistically infect both immunocompromised and immunocompetent individuals. The lungs are the primary site of infection and brain abscess is, by far, the most common complication following nocardial metastasis from pulmonary lesions. Although surgical intervention must always be considered in the treatment of nocardial brain abscess, it can obviously be cured by antibiotic therapy alone. This report describes a case infected by Nocardia cyriacigeorgica. Identification of the infectious agent was achieved by conventional and semi-nested PCR techniques. A 55-year-old woman with fever was referred to the infect disclinic of Imam Khomeini hospital in Tehran and was hospitalized after clinical assessment. She was a kidney transplant recipient for 4 years and was taking immunosuppressive treatment including azathioprine and methylprednisolone. Follow-up of the patient by CT scan revealed pulmonary infection and cerebral lesions. Specimens of the brain lesions contained filamentous bacteria. The patient received a combination of co-trimoxazole and ceftriaxone and brain abscesses as well as lung inflammation disappeared gradually during the course of antibiotic therapy within 3 months. The patient was discharged from the hospital after 2 months of therapy.