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Background: Nowadays, the emergence of methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant S. aureus (VRSA) strains has dramatically restricted the treatment options against this microorganism. Aim: In this study, we aimed to discover new drug targets and inhibitors against S. aureus. Methods: This study consists of two major sections. In the upstream evaluation, after a comprehensive coreproteome analysis, essential cytoplasmic proteins with no similarity to the human proteome were selected. Then the S. aureus metabolome-specific proteins were selected, and novel drug targets were identified using the DrugBank database. In the downstream analysis, a structure-based virtual screening approach was performed to reveal potential hit compounds against adenine N1 (m1A22)-tRNA methyltransferase (TrmK) using the StreptomeDB library and AutoDock Vina software. The compounds with a binding affinity > -9 kcal/mol were analyzed based on ADMET properties. Finally, the hit compounds were selected based on Lipinski’s rule of five (RO5). Results: Three proteins, including glycine glycosyltransferase (FemA), TrmK, and heptaprenyl pyrophosphate synthase subunit A (HepS1), were selected as feasible and promising drug targets based on PDB file availability and their essential role in the survival of the S. aureus. Finally, seven hit compounds, including Nocardioazine_ A, Geninthiocin_D, Citreamicin_delta, Quinaldopeptin, Rachelmycin, Di-AFN_A1 and Naphthomycin_ K were introduced against the binding cavity of TrmK, as a feasible drug target. Conclusion: The results of this study provided three feasible drug targets against S. aureus. In the following, seven hit compounds were introduced as potential inhibitors of TrmK, and Geninthiocin_D was identified as the most desirable agent. However, in vivo and in vitro investigations are needed to confirm the inhibitory effect of these agents on S. aureus.

Human monocytotropic ehrlichiosis is an emerging tick-borne infection caused by the obligate intracellular pathogen, Ehrlichia chaffeensis. The non-specific symptoms can range from a self-limiting fever to a fatal septic-like syndrome and may be misdiagnosed. The limited treatment choices including doxycycline are effective only in the initiation phase of the infection. It seems that novel therapeutic targets and new vaccine strategies could be effective to control this pathogen. This study is comprised of two major phases. First, the common proteins retrieved through subtractive analysis and potential drug targets were evaluated by subcellular localization, homology prediction, metabolic pathways, druggability, essentiality, protein-protein interaction networks, and protein data bank availability. In the second phase, surface-exposed proteins were assessed based on antigenicity, allergenicity, physiochemical properties, B cell and T cell epitopes, conserved domains, and protein-protein interaction networks. A multi-epitope vaccine was designed and characterized using molecular dockings and immune simulation analysis. Six proteins including WP_011452818.1, WP_011452723.1, WP_006010413.1, WP_006010278.1, WP_011452938.1, and WP_006010644.1 were detected. They belong to unique metabolic pathways of E. chaffeensis that are considered as new essential drug targets. Based on the reverse vaccinology, WP_011452702.1, WP_044193405.1, WP_044170604.1, and WP_006010191.1 proteins were potential vaccine candidates. Finally, four B cell epitopes, including SINNQDRNC, FESVSSYNI, SGKKEISVQSN, and QSSAKRKST, were used to generate the multi-epitope vaccine based on LCL platform. The vaccine showed strong interactions with toll-like receptors and acceptable immune-reactivity by immune simulation analysis. The findings of this study may represent a turning point in developing an effective drug and vaccine against E. chaffeensis. However, further experimental analyses have remained.

Background: Acinetobacter baumannii is an important nosocomial pathogen causing high morbidity and mortality in immunocompromised patients with prolonged hospitalization. Multidrug-resistant A. baumannii infections are on the rise worldwide. Therefore, the discovery of an effective vaccine against this bacterium seems necessary as a cost-effective and preventive strategy. Methods: In this present study, 35 genomes of A. baumannii strains were considered, and the extracellular proteins were selected, maximally having one transmembrane helix with high adhesion probability and no similarity to host proteins, as immunogenic candidates using the web tool Vaxign. Subsequently, the role of these selected proteins in bacterial pathogenesis was investigated using VICMpred. Then, the major histocompatibility complex class II, linear B-cell epitopes, and conservation of epitopes were identified using the Immune Epitope Database, BepiPred, and Epitope Conservancy Analysis, respectively. Finally, the B-cell discontinuous epitopes of each protein were predicted using ElliPro and plotted on the three-dimensional structure (3D) of the proteins. The role of the unknown proteins was predicted using the STRING database. Results: In this study, eight acceptable immunogenic candidates, including FilF, FimA, putative acid phosphatase, putative exported protein, subtilisin-like serine protease, and three uncharacterized proteins, were identified in A. baumannii. Conclusions: The results of the STRING database showed that these three uncharacterized proteins play a role in nutrition (heme utilization), peptide bond cleavage (serine peptidases), and cellular processes (MlaD protein). Extracellular proteins might play a catalyst role in the outer membrane protein-based vaccine of A. baumannii. Furthermore, this study proposed a list of potent immunogenic candidates of extracellular proteins.

The present study investigates the prevalence of Chlamydia trachomatis (CT), Neisseria gonorrhoeae (NG), and Trichomonas vaginalis (TV) among women with genitourinary infection and pregnancy-related complications in Tehran. It also evaluates the demographic information, symptoms, and sequelae. Endocervical samples were obtained over a period of eight months from 360 women including 180 symptomatic patients and 180 patients with pregnancy-related complications and infertility. CT, NG, and TV were detected in 10.8%, 6.9%, and 8.3% of all patients, respectively. The prevalence of CT, NG, and TV among women in the symptomatic group was 11.1%, 7.2%, and 13.3%, respectively, and among women with pregnancy-related complications and infertility was 10.6%, 6.7%, and 3.3%, respectively. Associations between chlamydia and ectopic pregnancy ( p = 0.001), and infertility ( p < 0.001) were observed. Abortion ( p = 0.008), infertility ( p = 0.005), and ectopic pregnancy ( p < 0.001) were associated with gonorrhea. Abnormal vaginal discharge ( p = 0.02) and vulvar itching ( p = 0.02) were associated with trichomoniasis. Overall, the prevalence rates of CT, NG, and TV were high in these patient groups. These high prevalences suggest that screening programs are required to reduce the burden of these sexually transmitted infections and their effects on genitourinary symptoms, pregnancy-related complications, and infertility.

Objectives: Increasing macrolide resistance of Mycoplasma pneumoniae strains is becoming a public health concern worldwide. Nevertheless, no comprehensive genomic background of circulating isolates...

Carbapenem-resistant Enterobacteriaceae (CRE) have been thoroughly studied as the pathogens associated with hospital acquired infections. However, data on Serratia marcescens are not enough. S. marcescens is now becoming a propensity for its highly antimicrobial-resistant clinical infections.Four carbapenem-resistant S. marcescens (CR-SM) isolates were obtained from hospitalized patients through routine microbiological experiments. We assembled the isolates genomes using whole genome sequencing (WGS) and compared their resistome and virulome patterns.The average length and CG content of chromosomes was 5.33 Mbp and 59.8%, respectively. The number of coding sequences (CDSs) ranged from 4,959 to 4,989. All strains had one single putative conjugative plasmid with IncL incompatibility (Inc) group. The strains harbored blaThe presence of conjugative plasmids harboring major β-lactamases within prophage and class 1 integron structures highlights the role of different mobile genetic elements (MGEs) in distribution of AMR factors and more specifically carbapenemases. More molecular studies are required to determine the status of carbapenem resistance in clinical starins. However, appropriate strategies to control the global dissemination of CR-SM are urgent.

Background Carbapenemase-producing Klebsiella pneumoniae (CP-KP) is becoming extensively disseminated in Iranian medical centers. Colistin is among the few agents that retains its activity against CP-KP. However, the administration of colistin for treatment of carbapenem-resistant infections has increased resistance against this antibiotic. Therefore, the identification of genetic background of co-carbapenem, colistin-resistance K.pneumoniae (Co-CCRKp) is urgent for implementation of serious infection control strategies. Methods Fourteen Co-CCRKp strains obtained from routine microbiological examinations were subjected to molecular analysis of antimicrobial resistance (AMR) using whole genome sequencing (WGS). Results Nine of 14 K.pneumoniae strains belonged to sequence type (ST)-11 and 50% of the isolates had K-locus type 15. All strains carried blaOXA-48 except for P26. blaNDM-1 was detected in only two plasmids associated with P6 and P26 strains belonging to incompatibility (Inc) groups; IncFIB, IncHI1B and IncFII. No blaKPC, blaVIM and blaIMP were identified. Multi-drug resistant (MDR) conjugative plasmids were identified in strains P6, P31, P35, P38 and P40. MICcolistin of K. pneumoniae strains ranged from 4 to 32 µg/ml. Modification of PmrA, PmrB, PhoQ, RamA and CrrB regulators as well as MgrB was identified as the mechanism of colistin resistance in our isolates. Single amino acid polymorphysims (SAPs) in PhoQ (D150G) and PmrB (R256G) were identified in all strains except for P35 and P38. CrrB was absent in P37 and modified in P7 (A200E). Insertion of ISKpn72 (P32), establishment of stop codon (Q30*) (P35 and P38), nucleotides deletion (P37), and amino acid substitution at position 28 were identified in MgrB (P33 and P42). None of the isolates were positive for plasmid-mediated colistin resistance (mcr) genes. P35 and P38 strains carried iutA, iucD, iucC, iucB and iucA genes and are considered as MDR-hypervirulent strains. P6, P7 and P43 had ICEKp4 variant and ICEKp3 was identified in 78% of the strains with specific carriage in ST11. Conclusion In our study, different genetic modifications in chromosomal coding regions of some regulator genes resulted in phenotypic resistance to colistin. However, the extra-chromosomal colistin resistance through mcr genes was not detected. Continuous genomic investigations need to be conducted to accurately depict the status of colistin resistance in clinical settings.

In this present study, 35 genomes ofIn this study, eight acceptable immunogenic candidates, including FilF, FimA, putative acid phosphatase, putative exported protein, subtilisin-like serine protease, and three uncharacterized proteins, were identified inThe results of the STRING database showed that these three uncharacterized proteins play a role in nutrition (heme utilization), peptide bond cleavage (serine peptidases), and cellular processes (MlaD protein). Extracellular proteins might play a catalyst role in the outer membrane protein-based vaccine of

Due to the emergence of multi-drug resistant Acinetobacter baumannii strains, there is an urgent need to develop several new strategies to control this bacterium. In this context, vaccination may be the best approach to reduce the morbidity and mortality associated with MDR isolates in vulnerable groups. Serum resistance factors have a key role in the pathogenesis of A. baumannii and can be considered as potential vaccine candidates. This project aimed to evaluate the immunological reactivity of CipA and PBP-7/8 as two serum resistance factors in a combination form against sepsis infections of A. baumannii. Recombinant proteins were obtained and immunological evaluations were performed against sepsis infection in the C57BL/6 mouse model. The data showed a statistically significant increase in total IgG levels in all three immunization regimens (CipA, PBP-7/8, and CipA + PBP-7/8) compared to the control group. The ratios of IgG2c/IgG1 in the CipA, PBP-7/8, and CipA + PBP-7/8 schedules were 8.7, 46.50, and 33.29, respectively. It appears that the immunization schedules developed a strong polarized Th1 response. The cytokine profiles of the three plans showed that IFN-γ was highly concentrated in the combination plan. However, the highest concentration of IL-17 belonged to the PBP-7/8 plan. In conclusion, the data of total IgG, survival rates and splenic bacterial loads showed that the CipA + PBP-7/8 plan was more effective than each protein individually.

Background The emergence of methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant S. aureus (VRSA) strains is a significant public health concern. Considering the high morbidity and mortality of invasive S. aureus infections and multi-drug resistant strains, there is an urgent need for non-antibiotic immune-based approaches to cure these infections. Despite all efforts, vaccine candidates targeting S. aureus failed in human clinical trials, and no approved vaccine is available against this pathogen. Therefore, this study aimed to introduce suitable candidates for immunization against S. aureus using a comprehensive reverse vaccinology approach. Methods In this study, we retrieved putative immunogenic targets from three different levels (literature review, automated reverse vaccinology, and manual reverse vaccinology) and evaluated them using several immunoinformatics analyses including antigenicity, allergenicity, PSI-BLAST to human proteome, physiochemical properties, B-cell, and T-cell epitopes. In the next step, the quartile method scoring was used to the shortlisted proteins. Finally, the molecular docking and immune simulation of immunogenic targets were performed for high prevalent sequence types. Results This study presents 12 vaccine candidates, including three enzymatic proteins (WP_000222271.1, WP_001170274, and WP_000827736.1), three cell wall-associated proteins (WP_001125631.1, WP_000731642, and WP_000751265.1), two hemolysins (WP_000594517.1, and WP_000916697.1), one secretion involved protein (WP_000725226.1), one heme‑iron binding protein (WP_001041573.1), one superantigen like protein (WP_000668994.1) and one hypothetical proteins (WP_000737711.1). Conclusion Through quartile scoring method, immune simulation and molecular docking, four promising targets including lytic transglycosylase IsaA, HlgA, secretory antigen precursor SsaA, and heme uptake protein IsdB were selected as the shortlisted proteins. It seems that a polarized immunization (Th1/Th17) response is needed for protection against this bacterium. An optimized formulation based on these putative immunogenic proteins and a wisely adjuvant selection may drive the immune system toward a full protection.

This study aimed to explore the prevalence, antimicrobial resistance levels, and serotype distribution of S. pneumoniae in the Middle East region. We conducted a systematic literature review by searching several databases including PubMed, ISI Web of Science, Scopus, Google scholar through 2000 to 2017 by using the following keywords: “Streptococcus pneumoniae”, “pneumococcus”, “serotype”, “Antibiotic resistance,” and “Middle East “in combination with “OR” and “AND” Boolean Operators within Title/Abstract/Keywords fields. We used a random-effects model to calculate the pooled prevalence and 95% confidence intervals (CIs) for binomial variables. All statistical analyses were done using STATA 12.0 (STATA Corp, College Station, TX). We found 73 articles appropriate, on the word of inclusion and exclusion criteria, for inclusion in this systematic review and meta-analysis. The result revealed that the pooled prevalence of S. pneumoniae carriage was 35% (95% CI: 26-44%). The most frequent pneumococcal serotypes were19, 19F, 6, 23 and 6A/B which were found in 19%,12%, 11%, 10% and 10% of isolates respectively. Pneumococcal resistance reported for azithromycin, cefaclor, clarithromycin, chloramphenicol, erythromycin, and tetracycline were 24%, 37%, 23%, 11%, 26%, and 29% respectively, while vancomycin resistance was not reported. The highest resistant prevalence was reported against co-trimoxazole (Trimethoprim/sulfamethoxazole). For this antibiotic, a pooled resistance prevalence of 43% was identified. The present review demonstrates that the prevalence of S. pneumoniae carriage was high in the Middle East region. Surveillance must be continued in this region to evaluate. The resistance pattern and serotype distribution.

Clostridioides difficile is one of the major causatives of nosocomial infections worldwide. Antibiotic-associated diarrhea, pseudomembranous colitis, and toxic megacolon are the most common forms of C. difficile infection (CDI). Considering the high antibiotic resistance of C. difficile isolates and the low efficacy of immunization with toxin-related vaccines, we suggested that surface-exposed and secreted proteins could be considered as potential immunogenic targets against CDI. Various immuninformatics databases were used to predict antigenicity, allergenicity, B-cell epitopes, MHC-II binding sites, conserved domains, prevalence and conservation of proteins among the most common sequence types, molecular docking, and immunosimulation of immunogenic targets. Finally, 16 proteins belonging to three functional groups were identified, including proteins involved in the cell wall and peptidoglycan layer (nine proteins), flagellar assembly (five proteins), spore germination (one protein), and a protein with unknown function. Molecular docking results showed that among all the mentioned proteins, WP_009892971.1 (Acd) and WP_009890599.1 (a C40 family peptidase) had the strongest interactions with human Toll-like receptor 2 (TLR-2) and TLR-4. This study proposes a combination of C. difficile toxoid (Tcd) and surface-exposed proteins such as Acd as a promising vaccine formulation for protection against circulating clinical strains of C. difficile.

Multi-drug resistance of Proteus mirabilis, a frequent cause of catheter-associated urinary tract infections, renders ineffective treatment. Therefore, new advanced strategies are needed to overcome it. In the meantime, vaccination may be the most effective and promising method. In this study antigenicity, allergenicity, subcellular localization, human homology, B-cell epitopes and MHC-II binding sites, conserved domains and protein-protein interactions were predicted using different reverse vaccinology methods and bioinformatics databases to find new putative immunogenic targets against P. mirabilis. Finally, 5 putative immunogenic targets against P. mirabilis were identified. Considering all criteria, QKQ94350.1 (Cell envelope opacity-associated protein A), QKQ94681.1 (Porin), QKQ95001.1 (TonB-dependent hemoglobin/ transferrin/ lactoferrin family receptor), QKQ95221.1 (AsmA) and QKQ94335.1 (N-acetylmuramoyl-L-alanine amidase) are excellent putative immunogenic targets. Finally, a multi-epitope vaccine was designed using the conserved linear epitopes of two OMPs (QKQ94681.1 and QKQ95001.1) and N-acetylmuramoyl-L-alanine amidase (QKQ94335.1), which have promising properties for immunization. These findings can simplify the development of efficient vaccines against P. mirabilis.

Background: Mycoplasma pneumoniae is a common cause of community-acquired pneumonia (CAP) worldwide, especially among children and debilitated populations. The present study aimed to investigate a loop-mediated isothermal amplification (LAMP) technique for rapid detection of M. pneumoniae in clini-cal specimens collected from patients with pneumonia. Methods: Throat swabs were collected from 110 outpatients who suffered from pneumonia. Throat swab samples were obtained from patients referred to the hospital outpatient clinics of Tehran University hospitals, Iran in 2017. The presence of M. pneumoniae in the clinical specimens was evaluated by LAMP, PCR and culture methods. Sensitivity and specificity of the LAMP and PCR assays were also determined. Results: Out of 110 specimens, LAMP assay detected M. pneumoniae in 35 specimens. Detection limit of the LAMP assay was determined to be 33fg /μL or ~ 40 genome copies/reaction. Moreover, no cross-reaction with genomic DNA from other bacteria was observed. Only 25 specimens were positive by the culture method. The congruence between LAMP assay and culture method was ‘substantial’ (κ=0.77). Specificity and sensitivity of LAMP assay were 88.2%, 100% in compare with culture. However, the con-gruence between LAMP assay and PCR assay was ‘almost perfect’ (κ=0.86). Specificity and sensitivity of LAMP assay were 92.5%, 100% in compare with PCR. Conclusion: Overall, the LAMP assay is a rapid and cost-efficient laboratory test in comparison to other methods including PCR and culture. Therefore, the LAMP method can be applied in identification of M. pneumoniae isolates in respiratory specimens.

Mycoplasma pneumoniae, Legionella pneumophila and Chlamydia pneumoniae are the most common bacterial agents, which account for 15–40%, 2–15% and 5–10% of atypical community-acquired pneumonia (CAP) respectively. These agents are mostly associated with infection in the outpatient setting. The aim of this study was to evaluate the frequency of these pathogens among patients with CAP attending outpatient clinics in Tehran. A cross-sectional study was carried out of 150 patients attending to educational hospitals in Tehran with CAP. M. pneumoniae, L. pneumophila and Chlamydia spp. were detected by PCR assay, targeting the P1 adhesion gene, macrophage infectivity potentiator (mip) gene and 16S rRNA gene respectively from throat swabs obtained from each patient. A total of 86 (57.3%) of 150 patients were women; median age was 50 years (interquartile range, 35–65 years). M. pneumoniae, L. pneumophila and Chlamydia spp. were detected in 37 (24.7%), 25 (16.7%) and 11 (7.3%) patients respectively; of these, 66 patients (44%) were infected at least by one of these three pathogens. The frequency of L. pneumophila was significantly higher among patients over 60 years old (p 0.03). Coinfection was detected in seven patients (4.7%); six were infected by M. pneumoniae and L. pneumophila, and only one was infected by L. pneumophila and Chlamydia spp. M. pneumoniae was the most prevalent agent of atypical CAP, and L. pneumophila was more likely to infect elderly rather than younger people. Further studies on the prevalence of CAP and its aetiologic agents are needed to improve the diagnosis and treatment of CAP patients.