Introduction of protein vaccine candidate based on AP65, AP33, and α-actinin proteins against Trichomonas vaginalis parasite: an immunoinformatics design

BACKGROUND

Trichomonas vaginalis is the most common nonviral sexually transmitted disease (STI) worldwide. Vaccination is generally considered to be one of the most effective methods of preventing infectious diseases. Using AP65, AP33 and α-actinin proteins, this research aims to develop a protein vaccine against Trichomonas vaginalis.

METHODS

Based on the B-cell and T-cell epitope prediction servers, the most antigenic epitopes were selected, and with the necessary evaluations, epitope-rich domains of three proteins, AP65, AP33, and α-actinin, were selected and linked. Subsequently, the ability of the vaccine to interact with toll-like receptors 2 and 4 (TLR2 and TLR4) was assessed. The stability of the interactions was also studied by molecular dynamics for a duration of 100 nanoseconds.

RESULTS

The designed protein consists of 780 amino acids with a molecular weight of 85247.31 daltons. The results of the interaction of the vaccine candidate with TLR2 and TLR4 of the immune system also showed that there are strong interactions between the vaccine candidate protein with TLR2 (-890.7 kcal mol-1) and TLR4 (-967.3 kcal mol-1). All parameters studied to evaluate the stability of the protein structure and the protein-TLR2 and protein-TLR4 complexes showed that the structure of the vaccine candidate protein is stable alone and in complex with the immune system receptors. Investigation of the ability of the designed protein to induce an immune response using the C-ImmSim web server also showed that the designed protein is capable of stimulating B- and T-cell lymphocytes to produce the necessary cytokines and antibodies against Trichomonas vaginalis.

CONCLUSIONS

Overall, our vaccine may have potential protection against Trichomonas vaginalis. However, for experimental in vivo and in vitro studies, it may be a good vaccine candidate.

Active site-based analysis of structural proteins for drug targets in different human Coronaviruses

Seven types of Coronaviruses (CoVs) have been identified that can cause infection in humans, including HCoV-229E, HCoV-NL63, HCoV-OC43, HCoV-HKU1, SARS-CoV, HCoV-MERS, and SARS-CoV-2. In this study, we investigated the genetic structure, the homology of the structural protein sequences, as well as the investigation of the active site of structural proteins. The active site of structural proteins was determined based on the previous studies, and the homology of their amino acid sequences and structure was compared. Multiple sequence alignment of Spike protein of HCoVs showed that the receptor-binding domain of SARS-CoV-2, SARS-CoV, and MERS-CoV was located at a similar site to the S1 subunit. The binding motif of PDZ (postsynaptic density- 95/discs large/zona occludens-1) of the envelope protein, was conserved in SARS-CoV and SARS-CoV-2 according to multiple sequence alignment but showed different changes in the other HCoVs. Overall, Spike protein showed the most variation in its active sites, but the other structural proteins were highly conserved. In this study, for the first time, the active site of all structural proteins of HCoVs as a drug target was investigated. The binding site of these proteins can be suitable targets for drugs or vaccines among HCoVs.

Antimicrobial resistance patterns and phylogenetic analysis of Shiga toxin-producing Escherichia coli strains from goats using both Clermont phylogenetic schemes

Foodborne transmission of Shiga toxin-producing Escherichia coli (STEC) poses a threat to public health. The Clermont typing schemes (previous and revised) have been used widely to phylotype E. coli. The present study was conducted to compare the relationship of the Clermont phylogenet-ic schemes in STEC strains isolated from goats and antibiotic resistance patterns in the southeast of Iran. Overall 52 strains carrying the stx gene were used for subsequent analysis. All strains were determined by analysing the genomic DNA with a PCR-based method using the two Clermont et al. (2000, 2013) schemes. Extended spectrum beta-lactamase (ESBL) producing strains were con-firmed by the double disk-diffusion method. STEC strains were also tested for susceptibility to 20 antimicrobials agents. In the original Clermont method, the prevalent phylogroups were B1 (69.2%) and A (28.8%). The significant phylogenetic groups of strains according to the revised Clermont method were B1 (82.7%), A (13.5%) and unknown (3.8%). However, STEC strains underwent changes as noted from A to B1 (17.3%), B1 to unknown (3.8%), B1 to A (1.9%) and D to B1 (1.9%) groupings. Of the 52 stx-positive strains, two ESBL producing strains were detected. Susceptibility data showed that the most frequent resistance phenotype was related to cefazolin (90.4%), streptomycin (88.5%), ampicillin (86.5%) and oxytetracycline (82.7%) respectively. Alt-hough the overall frequency of the reassigned phylotypes was not significant, most changes oc-curred within the A phylotype. Therefore, implementation of the new method on isolates belong-ing to the A phylotype in the old method seems to be necessary to obtain accurate results.

Antibacterial Effect of Low-Level Laser (Diode 405 nm) on Antibiotic-Resistant Enterococci Clinical Isolates (In Vitro)

Background: Enterococcus is a part of normal gastrointestinal flora in human body. Nevertheless, antibiotic-resistant Enterococcus (ARE) is considered a key factor in nosocomial infections which result in a considerable increase in the rate of patient death due to referring of numerous patients to health centers annually, or lead to extended disease convalescence. Objective: This study aimed to evaluate the bactericidal effect at 405nm diode at a laser power of 30 mW on ARE viability of clinical infections. Materials and Methods: In the present study, 30 isolates underwent antibiotic susceptibility test (AST) in which sensitivity to piperacillin (100 µg), rifampin (5 µg), and oxacillin (1 µg) were measured based on the Clinical and Laboratory Standards Institute (CLSI) guidelines. Afterwards, ten most resistant isolates were selected and irradiated by a 405 nm diode laser at a power of 30 mW for 180 and 240 seconds. The data were reported statistically as mean ± standard deviation, and the analysis of the data on varied bacteria was performed using ANOVA. The result was evaluated by SPSS software and P value ≤0.05 was interpreted to be significant. Results: Bacterial viability decreased unsteadily to 10 resistant isolates. Moreover, enhancing irradiation time caused a lower viability rate in such a way that the viability of isolate 9 having the lowest viability rate was reduced from 2.94% in 180 seconds to 0.58% in 240 seconds. The result was evaluated by SPSS software and P value was determined to be significant, and P≤0.05 was laser irradiation for either 180 s or 240 s. Conclusion: Following the study results, 405 nm diode laser could be applied as a tool for eliminating clinical ARE, and it was useful for preventing hospital-acquired infections.

The complex genetic region conferring transferable antibiotic resistance in multidrug-resistant and extremely drug-resistant Klebsiella pneumoniae clinical isolates

Antibiotic resistance due to transferable resistance genes is one of the most important concerns in Klebsiella pneumoniae isolated from nosocomial infections. Eighty-eight K. pneumoniae isolates were confirmed through biochemical methods. In addition, antimicrobial susceptibility testing was performed using a disc-diffusion method. Extended-spectrum β-lactamase production among the isolates was screened using a double-disc synergism test, and the resistance genes were identified using PCR. The eight loci for multiple-locus variable number tandem repeat analysis (MLVA) genotyping were selected along with the primers. According to our findings, neomycin (5; 5.6%) and carbapenems (10; 11.3%) showed the most remarkable inhibitory effect but co-trimoxazole (46; 52.2%) was the least effective antibiotic against K. pneumoniae isolates. bla _CTX-M-1 , qnrA, qnrB, qnrS, intI, intII, aac3 and aac6 were detected in 30 (34%), 5 (5.6%), 29 (32.9%), 23 (26.1%), 88 (100%), 72 (81.8%), 26 (29.5%) and 28 (31.8%) of the 88 isolates, respectively. But none of the K. pneumoniae isolates expressed the intIII gene. Using MLVA, 23 MLVA types and eight clusters were identified. Extended-spectrum β-lactamase-producing K. pneumoniae isolates were classified into two clonal complexes. Effective strategies for infection control should be applied to monitor and control the spread of multidrug-resistant isolates by the resistance genes located on the mobile genetic elements.

Reverse vaccinology approach to design a novel multi-epitope vaccine candidate against COVID-19: an in silico study

At present, novel Coronavirus (2019-nCoV, the causative agent of COVID-19) has caused worldwide social and economic disruption. The disturbing statistics of this infection promoted us to develop an effective vaccine candidate against the COVID-19. In this study, bioinformatics approaches were employed to design and introduce a novel multi-epitope vaccine against 2019-nCoV that can potentially trigger both CD⁴⁺ and CD⁸⁺ T-cell immune responses and investigated its biological activities by computational tools. Three known antigenic proteins (Nucleocapsid, ORF3a, and Membrane protein, hereafter called NOM) from the virus were selected and analyzed for prediction of the potential immunogenic B and T-cell epitopes and then validated using bioinformatics tools. Based on in silico analysis, we have constructed a multi-epitope vaccine candidate (NOM) with five rich-epitopes domain including highly scored T and B-cell epitopes. After predicting and evaluating of the third structure of the protein candidate, the best 3 D predicted model was applied for docking studies with Toll-like receptor 4 (TLR4) and HLA-A*11:01. In the next step, molecular dynamics (MD) simulation was used to evaluate the stability of the designed fusion protein with TLR4 and HLA-A*11:01 receptors. MD studies demonstrated that the NOM-TLR4 and NOM-HLA-A*11:01 docked models were stable during simulation time. In silico evaluation showed that the designed chimeric protein could simultaneously elicit humoral and cell-mediated immune responses. Communicated by Ramaswamy H. Sarma.

Significant spread of extensively drug-resistant Acinetobacter baumannii genotypes of clonal complex 92 among intensive care unit patients in a university hospital in southern Iran

PURPOSE

Infections associated with Acinetobacter baumannii represent an increasing threat in healthcare settings. Therefore, we investigated the epidemiological relationship between clinical isolates of A. baumannii obtained from patients in a university hospital in Bandar Abbas in southern Iran.

METHODOLOGY

Sixty-four consecutive non-duplicate clinical isolates collected during 2014-2015 were subjected to susceptibility testing, clonal relationship analysis using PFGE, multilocus variable-number tandem-repeat analysis (MLVA) and multilocus sequence typing (MLST), and examined for the presence of carbapenemases and integrons.

RESULTS

Almost all A. baumannii isolates were extensively drug-resistant (XDR; 98 %) and carried an OXA carbapenemase gene (blaOXA-23-like; 98 %) and class 1 integrons (48 %). PFGE and MLST analysis identified three major genotypes, all belonging to clonal complex 92 (CC92): sequence type 848 (ST848) (n=23), ST451 (n=16) and ST195 (n=8). CC92 has previously been documented in the hospital setting in northern Iran, and ST195 has been reported in Arab States of the Persian Gulf. These data suggest national and global transmission of A. baumannii CC92.

CONCLUSION

This report demonstrates the occurrence and potential spread of closely related XDR genotypes of A. baumannii CC92 within a university hospital in southern Iran. These genotypes were found in the majority of the investigated isolates, showed high prevalence of blaOXA-23 and integron class 1, and were associated with stay in the intensive care unit. Very few treatment options remain for healthcare-adapted XDR A. baumannii, and hence effective measures are desperately needed to reduce the spread of these strains and resultant infections in the healthcare setting.

Identification of Carbapenem-Resistant Klebsiella pneumoniae with Emphasis on New Delhi Metallo-Beta-Lactamase-1 (blaNDM-1) in Bandar Abbas, South of Iran

BACKGROUND AND OBJECTIVE

The spread of carbapenem-resistant Klebsiella pneumoniae especially bla_NDM-1-carrying isolates is a great concern worldwide. In this study we describe the molecular basis of carbapenem-resistant K. pneumoniae in three teaching hospitals at Bandar Abbas, south of Iran.

MATERIALS AND METHODS

A total of 170 nonduplicate clinical isolates of K. pneumoniae were investigated. Antimicrobial susceptibility test was performed by disc diffusion method. PCR was carried out for detection of carbapenemase (bla_KPC, bla_IMP, bla_VIM, bla_NDM, bla_SPM, bla_OXA-48, and bla_OXA-181) and extended-spectrum β-lactamase (bla_CTX-M, bla_SHV, bla_TEM, bla_VEB, bla_GES, and bla_PER). Clonal relatedness of bla_NDM-1-positive isolates was evaluated by multilocus sequence typing (MLST).

RESULTS

Tigecycline was the most effective antimicrobial agent with 96.5% susceptibility. In addition, 6.5% of the isolates were carbapenem resistant. Bla_NDM-1 was identified in four isolates (isolate A-D) and all of them were multidrug-resistant. MLST revealed that bla_NDM-1-positive isolates were clonally related and belonged to two distinct clonal complexes, including sequence type (ST) 13 and ST 392. In addition to bla_NDM-1, isolate A coharbored bla_SHV-11, bla_CTX-M-15, and bla_TEM-1, isolate B harbored bla_SHV-11 and bla_CTX-M-15, and isolates C and D contained both bla_SHV-1 and bla_CTX-M-15.

CONCLUSION

Our results indicate that NDM-1-producing K. pneumoniae ST 13 and ST 392 are disseminated in our region. Moreover, one of our major concerns is that these isolates may be more prevalent in the near future. Tracking and urgent intervention is necessary for control and prevention of these resistant isolates.

In vitro activity of linezolid alone and combined with other antibiotics against clinical enterococcal isolates

BACKGROUND

The increasing incidence of antimicrobial resistance has led to research on finding new antimicrobial agents or identifying drug combinations with synergistic effects. Enterococcal infections, particularly those associated with vancomycin-resistant enterococci (VREs), are therapeutic problems. Linezolid (LZD), an oxazolidinone antibiotic, shows good activity against Gram-positive bacteria including enterococci. To avoid the emergence of linezolid-resistant subpopulations and achieve enhanced activity or bactericidal effect, the use of combined therapy has been considered.

METHODS

The in vitro activity of LZD in combination with five different antibiotics was evaluated using a microdilution checkerboard method and time-kill study against 12 clinical enterococcus isolates.

RESULTS

With the checkerboard method, LZD plus doxycycline (DX) had the highest frequency among all synergistic combinations. This combination and the one of LZD plus ceftriaxone (CRO) were the most frequent effective combinations against VREs. Time-kill studies using selected synergistic combinations-LZD + DX and LZD + CRO-showed an indifferent interaction. One tested combination of LZD + rifampicin showed antagonism.

CONCLUSIONS

Antagonistic interactions in combinations containing LZD are rare. LZD + DX and LZD + CRO may be beneficial in the treatment of VREs. However, more time-kill studies as well as in vivo experiments are required.

Molecular characterization of nasal methicillin resistant Staphylococcus aureus isolates from workers of an automaker company in southeast Iran

Colonization of methicillin resistant Staphylococccus aureus (MRSA) can occur more commonly in healthy people who live in close together or are in close physical contact with each other. Having knowledge about the molecular characteristics of these strains provides considerable discernment into the epidemiology of this important microorganism. A total of 806 nasal swabs were collected from healthy workers of an automaker company in the southeast of Iran and were analyzed to detect MRSA isolates. Multilocus sequence typing (MLST), spa typing, and detection of staphylococcal cassette chromosome mec (SCCmec) were performed. The presence of genes encoding Panton-Valentine Leukocidin (PVL) and Arginine Catabolic Mobile Element (ACME) were also investigated. Carriage rate of S. aureus was 20%. Among 10 identified MRSA, no acme was found while high prevalence of pvl (60%) was of great concern. Seven different spa types including five new ones were identified. The most frequent sequence type was the novel one; ST 3373 (n = 3), followed by each of ST22, ST88, ST859 (n = 2) and ST1955 (n = 1). MRSA isolates were clustered into two main clonal complexes; CC22 (n = 6) and CC88 (n = 4). Low genetic diversity with the dominance of CC22, SCCmecIV was found. Distribution of previously found hospital-associated MRSA was demonstrated among our isolates.

Incidence of Hospital-Acquired Bacterial Pneumonia and Its Resistance Profiles in Patients Admitted to Intensive Care Unit

<p>Hospital-acquired bacterial pneumonia (HABP) is one of the most important causes of morbidity, mortality and economic problems especially for patients admitted in the intensive care unit (ICU) ward. The aim of this study was to determine the incidence of nosocomial pneumonia in ICU, identify the causative bacteria and their resistance profiles. This cross sectional study was performed on 214 patients who were admitted in the ICU ward of a general hospital requiring mechanical ventilation for at least 48 h. Identification of HABP was based on the clinical signs manifested 48 h or more after admission, new chest X-ray infiltrates and microbiologic examination of endo tracheal secretion. Data were analyzed using SPSS 21 to perform the descriptive statistics. The isolated gram negative bacteria were <em>Klebsiella pneumoniae</em> (50%), <em>Staphylococcus aureus</em> (18.7%), <em>Acinetobacter baumannii</em> (12.5%), <em>Escherichia coli</em> (12.5%) and <em>Pseudomonas aeroginosa</em> (6.3%). The maximum antimicrobial resistance of gram negative bacteria was to Cefazolin (100%) and Ampicillin (84.6%), while antimicrobial resistance to Clindamycin, Azithromycin, Amoxycillin+clavulanate, Trimethoprim+sulfamethoxazole and Ciprofloxacin was 33.3%. No resistance was seen towards carbapenems.The most frequent gram negative isolated bacterium was <em>K. pneumoniae, </em>and maximum antimicrobial resistance rate was observed for Cefazolin and Ampicillin, which is due to betalactamase production.</p>

Seasonal Distribution of Fungi in Soil Found in Two Hospitals in Bandar Abbas, Iran

INTRODUCTION

Fungal contamination in hospitals has been a major health concern, especially in immunosuppressed patients. Construction programs increase the risk of fungal contaminations in hospitals. This study aimed to monitor and compare fungal contamination in two hospitals in Bandar Abbas, Iran, one of which was undergoing construction. Furthermore, the study determined the seasonal variations in the prevalence of fungi identified in the two hospitals.

METHODS

This study was conducted during April-December 2014 on 146 soil samples collected from the Shahid Mohammadi Hospital that was under construction and the Shariati Hospital that was not involved in any construction program. The soil samples were collected in the morning from the dust on the ground. Statistical analysis was performed using the chi-squared test.

RESULTS

Among the fungal cultures, 83.56% were found to be positive. We identified 122 fungal isolates, representing 16 genera, 13 of the genera were isolated from Shahid Mohammadi Hospital and 14 were isolated from Shariati Hospital. Aspergillus was the dominant fungus in both hospitals. In Shariati Hospital, 100% of Aspergiluss niger were isolated in the summer. In the spring, Mocur was dominant in both hospitals, and, in the winter, Rhizopus spp. was the dominant fungus in Shahid Mohammadi Hospital (55.5%); however, this fungus was dominant in spring in Shariati Hospital (66.7%). In Shariati Hospital, Scopulariopsis, Drechslera, Penicillium spp., and Yeasts were present only in the fall, whereas yeast was the dominant fungus in summer (100%) in Shahid Mohammadi Hospital. There were not significant differences between two hospitals, with the exception of Fusarium spp., which was more frequent in Shariati Hospital, where no renovation was taking place (p = 0.008).

CONCLUSION

Our results indicated that specific ecological niches existed in the two general hospitals in Bandar Abbas. Special attention should be paid to environmental control programs. It is recommended that soil exposure be considered in patients' histories in addition to the current focus on infections related to food and water.

Molecular Identification of Resistance Determinants, Integrons and Genetic Relatedness of Extensively Drug Resistant Acinetobacter baumannii Isolated From Hospitals in Tehran, Iran

Background:

Acinetobacter baumannii has emerged as an important nosocomial pathogen. Hospital outbreaks of extensively drug resistant (XDR) A. baumannii are a great concern.

Objectives:

Aims of this study were to characterize the resistance determinants and genetic relatedness of (XDR) A. baumannii isolates in hospitals in Tehran, Iran.

Materials and Methods:

During a three-year study, clinical isolates of A. baumannii were collected from two hospitals in Tehran, Iran. Susceptibility testing to antibiotics was performed by disk diffusion method and XDR A. baumannii isolates were identified. Genes’ encoding for carbapenemase production and integrons were identified by PCR. MICs of imipenem and meropenem were determined by agar dilution. Multiple locus variable-number tandem repeat analysis (MLVA) typing was used to determine genetic relationships of XDR isolates.

Results:

Using PCR for amplification of bla_OXA-51, 93.9% (123.131) of isolates were identified as A. baumannii and 24.4% (30.123) were XDR. These isolates were resistant to gentamicin, ciprofloxacin, amikacin, cotrimoxazole, cefepime, cefotaxime, aztreonam and ceftazidime. Thirty percent of the isolates were resistant to tigecycline. All isolates were susceptible to colistin and polymyxin-B, while 93.3% (28.30) possessed bla_OXA-23-like and 6.7% (2.30) possessed bla_OXA-24-like. All isolates possessed insertion sequence (ISAba1) in the upstream region of the _OXA-23-like gene. Almost 96.7% (29.30) of the isolates were positive for class I integron and 43.3% (13.30) for class II. These isolates were also positive for class I. Class III integron was not detected. MLVA typing of XDR isolates showed seven clonally complexes and 16 singletons.

Conclusions:

The population structure of the A. baumannii isolates in our hospitals was genetically diverse. A significant association between XDR pattern and presence of class 1 integron (P < 0.001) was found indicating that many antibiotic resistance determinants are involved in development of XDR strains.

In Vitro Activity of Tigecycline and Colistin against clinical isolates of Acinetobacter baumannii in Hospitals in Tehran and Bandar-Abbas, Iran

Background:

The Acinetobacter species, particularly A. baumannii, has emerged as one of the main causes of nosocomial infections in recent years. The high prevalence of drug resistance in A. baumannii limits the therapeutic options for treating infections caused by these bacteria. The objective of this study was to determine the in vitro activity of Tigecycline and Colistin against clinical isolates of A. baumannii in Tehran and Bandar Abbas, Iran.

Methods:

This study was conducted from March 2009 to November 2010 at three hospitals in Tehran and Bandar Abbas, Iran, using 165 Acinetobacter species isolated from clinical specimens. All isolates were subjected to PCR to detect bla_OXA-51-like genes that are unique to Acinetobacter baumannii. Isolates that gave a band for the bla_OXA-51-like genes were identified as A. baumannii. Anti-microbial susceptibility tests were performed for Tigecycline, Colistin, and other antibiotics.

Results:

Sensitivity rates to Colistin and Polymyxin-B were 100%. Resistance rates for Tigecycline were 4.2% in Tehran and 8.8% in Bandar-Abbas according to Jones criteria, whereas, according to U.S. FDA criteria, the resistance rates were 20.8% and 17.6%, respectively.

Conclusions:

New alternative drugs are needed for the treatment of drug resistant A. baumannii. Although Colistin appears to be a good choice, adverse reactions have limited its usage. Tigecycline is effective against A. baumannii isolates, and it shows promise for solving the problem.