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1.
Med Princ Pract ; 33(3): 185-197, 2024.
Article in English | MEDLINE | ID: mdl-38402870

ABSTRACT

The success in determining the whole genome sequence of a bacterial pathogen was first achieved in 1995 by determining the complete nucleotide sequence of Haemophilus influenzae Rd using the chain-termination method established by Sanger et al. in 1977 and automated by Hood et al. in 1987. However, this technology was laborious, costly, and time-consuming. Since 2004, high-throughput next-generation sequencing technologies have been developed, which are highly efficient, require less time, and are cost-effective for whole genome sequencing (WGS) of all organisms, including bacterial pathogens. In recent years, the data obtained using WGS technologies coupled with bioinformatics analyses of the sequenced genomes have been projected to revolutionize clinical bacteriology. WGS technologies have been used in the identification of bacterial species, strains, and genotypes from cultured organisms and directly from clinical specimens. WGS has also helped in determining resistance to antibiotics by the detection of antimicrobial resistance genes and point mutations. Furthermore, WGS data have helped in the epidemiological tracking and surveillance of pathogenic bacteria in healthcare settings as well as in communities. This review focuses on the applications of WGS in clinical bacteriology.


Subject(s)
Whole Genome Sequencing , Humans , Whole Genome Sequencing/methods , Genome, Bacterial , Drug Resistance, Bacterial/genetics , High-Throughput Nucleotide Sequencing/methods
2.
Med Princ Pract ; : 1-17, 2024 Oct 30.
Article in English | MEDLINE | ID: mdl-39476812

ABSTRACT

OBJECTIVE: In this study, we have mapped the relative importance of well-defined recombinantly expressed Mycobacterium tuberculosis antigens in the T cell recognition repertoire of latently infected individuals not progressing to active disease. MATERIALS AND METHODS: Peripheral blood mononuclear cells from healthy latently infected long term non-progressors were screened for antigen-induced proliferation and Th1 cytokine, Interferon- (IFN-γ) responses. RESULTS: The panel of antigens tested showed a clear spectrum of responsiveness and lead to the identification of a subgroup of frequently recognized antigens (MPT59, CFP7, CFP10, CFP21, TB37.6 /PPE68, ESAT-6, MPT51, and DnaK) with a high cellular response level as measured in both proliferation and IFN-γ assays. Among a subgroup of antigens also screened for responses in tuberculosis patients, CFP21 was identified as differentially recognized in non-progressors. For both cellular assays, we found a positive correlation between responder frequency and magnitude of response. A significant correlation between the level of antigen-specific proliferation and INF-γ secretion was also observed. CONCLUSION: We have identified a defined set of M. tuberculosis antigens frequently recognized by T cells at a high response level from latently infected long term non-progressors which warrant further investigation for a potential role in immune regulation and protection against progression to active disease.

3.
Med Princ Pract ; 33(1): 66-73, 2024.
Article in English | MEDLINE | ID: mdl-38147830

ABSTRACT

OBJECTIVE: Workers in the healthcare sector are exposed to a multitude of bacterial genera. The location of their work contributes significantly to shaping personal microbiomes. In this study, we investigated the role of the workspace on the nasal bacteriome of staff working in a healthcare-associated research facility. METHODS: The anterior nares of 10 staff working in different laboratories on the ground and first floor of the research facility were aseptically swabbed. Genomic DNA from each sample was used to amplify the V3 and V4 regions of the 16S rRNA gene. The amplified products were sequenced using the MiSeq sequencer (Illumina). Operational taxonomic units were filtered through MG-RAST v.3.6. Taxonomic profiling and visualizations were performed in MicrobiomeAnalyst v2.0. RESULTS: The Wilcoxson Sum test at median abundances (p < 0.05) indicated that seven taxa (Micromonosporaceae, Micromonospora, Lactobacillaceae, Lactobacillus, Betaproteobacteria, Burkholderiales, Pectobacterium) were significantly diverse between ground-floor and first-floor workers. The analysis of similarity coefficient was 0.412 (p < 0.03) between the ground and the first-floor workers. Random forest analysis predicted 15 features that were significantly different (p < 0.05) in individuals working in different laboratories. Species richness and evenness also differed according to the placement of individuals in respective laboratories. CONCLUSION: These findings add to the knowledge that the healthcare support staff are at a speculated occupational risk. A slight shift in the abundances of bacterial genera and species might lead to unwanted consequences. Continual monitoring is thus warranted.


Subject(s)
Microbiota , Humans , RNA, Ribosomal, 16S/genetics , Microbiota/genetics , Bacteria/genetics , Health Personnel , Delivery of Health Care
4.
BMC Biotechnol ; 23(1): 26, 2023 07 31.
Article in English | MEDLINE | ID: mdl-37525145

ABSTRACT

Oxford Nanopore sequencing technology (ONT) is currently widely used due to its affordability, simplicity, and reliability. Despite the advantage ONT has over next-generation sequencing in detecting resistance genes in mobile genetic elements, its relatively high error rate (10-15%) is still a deterrent. Several bioinformatic tools are freely available for raw data processing and obtaining complete and more accurate genome assemblies. In this study, we evaluated the impact of using mix-and-matched read assembly (Flye, Canu, Wtdbg2, and NECAT) and read correction (Medaka, NextPolish, and Racon) tools in generating complete and accurate genome assemblies, and downstream genomic analysis of nine clinical Escherichia coli isolates. Flye and Canu assemblers were the most robust in genome assembly, and Medaka and Racon correction tools significantly improved assembly parameters. Flye functioned well in pan-genome analysis, while Medaka increased the number of core genes detected. Flye, Canu, and NECAT assembler functioned well in detecting antimicrobial resistance genes (AMR), while Wtdbg2 required correction tools for better detection. Flye was the best assembler for detecting and locating both virulence and AMR genes (i.e., chromosomal vs. plasmid). This study provides insight into the performance of several read assembly and read correction tools for analyzing ONT sequencing reads for clinical isolates.


Subject(s)
Genomics , Virulence Factors , Virulence Factors/genetics , Reproducibility of Results , Escherichia coli/genetics , High-Throughput Nucleotide Sequencing , Drug Resistance , Sequence Analysis, DNA
5.
Med Princ Pract ; 2023 Sep 13.
Article in English | MEDLINE | ID: mdl-37703836

ABSTRACT

Early Secreted Antigenic Target 6 kDa (ESAT6) is a potent immunogenic protein secreted by the bacteria causing tuberculosis, i.e., Mycobacterium tuberculosis. Another highly immunogenic culture filtrate protein whose gene is linked to ESAT6/ESXA is known as CFP10/ESXB. Because of their high immunogenicity and specificity to M. tuberculosis, these proteins have been proposed as a vaccine to prevent tuberculosis and diagnose the active/latent disease. However, the same proteins cannot be used for prevention and diagnosis because immunized but healthy people will also show a positive response and be falsely reported as diseased. Therefore, in this review article, the search was made to identify if any other ESAT6-like proteins exist in the M. tuberculosis genome. The search identified 21 additional ESAT-like proteins, i.e., ESXC to ESXW. Immunological characterization has shown that some of them (especially ESXV) were able to induce immune responses in vitro with cells obtained from tuberculosis patients and healthy donors. When the protein ESXV was tested in different recombinant forms (expressed in Escherichia coli, mycobacterial vectors, and DNA plasmids) and injected in mice, immune responses were induced to multiple epitopes of the protein. Furthermore, immunization of mice with ESXV protected them from infection with M. tuberculosis. The same protein was also able to protect mice against the induction of asthma. These results suggest that ESXV has the potential to protect against two major diseases of the world, i.e., tuberculosis and asthma, and hence may be used as a common vaccine for both diseases.

6.
Med Princ Pract ; 31(4): 359-367, 2022.
Article in English | MEDLINE | ID: mdl-35584661

ABSTRACT

OBJECTIVE: This study determined the effects of chemical adjuvants, incomplete Freund's adjuvant (IFA) and aluminum hydroxide (Alum), mycobacteria, and a DNA plasmid as delivery systems on the induction of protective Th1 (interferon-gamma (IFN-γ)) and nonprotective Th2 (IL-5) and Treg (IL-10) cytokine responses to Rv3619c and its peptides. Rv3619c is an immunodominant Mycobacterium tuberculosis-specific antigen and belongs to the early-secreted antigenic target of 6 kDa-family of proteins. Delivery systems are needed to deliver such antigens in animal models and induce protective immune responses. METHODS: The rv3619c gene was amplified from the genomic DNA of M. tuberculosis and cloned into appropriate vectors for expression in Escherichia coli, Mycobacterium smegmatis, and eukaryotic cells. Spleen cells from mice immunized with rv3619c using different delivery systems were stimulated in vitro with synthetic peptides (P1 to P6) of Rv3619c, and secreted cytokines were estimated by ELISA. RESULTS: The recombinant M. smegmatis and DNA plasmid induced the secretion of the protective cytokine IFN-γ in response to peptide-pool of Rv3619c and all the individual peptides, whereas rv3619c/IFA induced the secretion of IFN-γ in response to the peptide pool, and the peptides P5 and P6. However, the secretions of the nonprotective cytokines IL-5 and IL-10 were induced to none of the peptides with the delivery systems used. CONCLUSION: Rv3619c is a major antigen of M. tuberculosis with multiple immunogenic epitopes; however, immune responses to individual epitopes can vary based on delivery systems used.


Subject(s)
Antigens, Bacterial/pharmacology , Bacterial Proteins/pharmacology , Mycobacterium tuberculosis , Tuberculosis , Animals , Antigens, Bacterial/genetics , Antigens, Bacterial/metabolism , Bacterial Proteins/genetics , Cytokines/metabolism , Epitopes/metabolism , Interferon-gamma/metabolism , Interleukin-10/metabolism , Interleukin-5/metabolism , Mice , Peptides/metabolism , Recombinant Proteins , Th1 Cells/metabolism , Tuberculosis/metabolism , Tuberculosis/prevention & control
7.
Ann Clin Microbiol Antimicrob ; 19(1): 56, 2020 Nov 30.
Article in English | MEDLINE | ID: mdl-33256750

ABSTRACT

At the time of writing, the SARS-CoV-2 virus has infected more than 49 million people causing more than 1.2 million deaths worldwide since its emergence from Wuhan, China in December 2019. Vaccine development against SARS-CoV-2 has drawn the global attention in order to stop the spread of the virus, with more than 10 vaccines being tested in phase III clinical trials, as of November 2020. However, critical to vaccine development is consideration of the immunological response elicited as well as biological features of the vaccine and both need to be evaluated thoroughly. Tuberculosis is also a major infectious respiratory disease of worldwide prevalence and the vaccine development for tuberculosis has been ongoing for decades. In this review, we highlight some of the common features, challenges and complications in tuberculosis vaccine development, which may also be relevant for, and inform, COVID-19 vaccine development.


Subject(s)
COVID-19 Vaccines/immunology , COVID-19/prevention & control , SARS-CoV-2/immunology , Tuberculosis Vaccines/immunology , COVID-19/etiology , COVID-19/transmission , COVID-19 Vaccines/adverse effects , Humans
8.
Med Princ Pract ; 29(5): 404-411, 2020.
Article in English | MEDLINE | ID: mdl-32422630

ABSTRACT

Asthma is a cause of substantial burden of disease in the world, including both premature deaths and reduced quality of life. A leading hypothesis to explain the worldwide increase of asthma is the "hygiene hypothesis," which suggests that the increase in the prevalence of asthma is due to the reduction in exposure to infections/microbial antigens. In allergic asthma, the most common type of asthma, antigen-specific T helper (Th)2 and Th17 cells and their cytokines are primary mediators of the pathological consequences. In contrast, Th1 and T regulatory (Treg) cells and their cytokines play a protective role. This article aims to review the information on the effect of mycobacteria and their antigens in modulating Th2/Th17 responses towards Th1/Treg responses and protection against asthma in humans and animal models.


Subject(s)
Asthma/immunology , Asthma/prevention & control , Bacterial Vaccines/administration & dosage , Bacterial Vaccines/immunology , Mycobacterium/immunology , Animals , Antigens, Bacterial , BCG Vaccine/administration & dosage , BCG Vaccine/immunology , Cytokines/metabolism , Humans , Inflammation Mediators/metabolism , T-Lymphocytes, Helper-Inducer/metabolism , T-Lymphocytes, Regulatory/metabolism
9.
J Med Virol ; 90(3): 412-420, 2018 03.
Article in English | MEDLINE | ID: mdl-29083040

ABSTRACT

A metagenomic approach based on target independent next-generation sequencing has become a known method for the detection of both known and novel viruses in clinical samples. This study aimed to use the metagenomic sequencing approach to characterize the viral diversity in respiratory samples from patients with respiratory tract infections. We have investigated 86 respiratory samples received from various hospitals in Kuwait between 2015 and 2016 for the diagnosis of respiratory tract infections. A metagenomic approach using the next-generation sequencer to characterize viruses was used. According to the metagenomic analysis, an average of 145, 019 reads were identified, and 2% of these reads were of viral origin. Also, metagenomic analysis of the viral sequences revealed many known respiratory viruses, which were detected in 30.2% of the clinical samples. Also, sequences of non-respiratory viruses were detected in 14% of the clinical samples, while sequences of non-human viruses were detected in 55.8% of the clinical samples. The average genome coverage of the viruses was 12% with the highest genome coverage of 99.2% for respiratory syncytial virus, and the lowest was 1% for torque teno midi virus 2. Our results showed 47.7% agreement between multiplex Real-Time PCR and metagenomics sequencing in the detection of respiratory viruses in the clinical samples. Though there are some difficulties in using this method to clinical samples such as specimen quality, these observations are indicative of the promising utility of the metagenomic sequencing approach for the identification of respiratory viruses in patients with respiratory tract infections.


Subject(s)
Respiratory Tract Infections/diagnosis , Respiratory Tract Infections/virology , Viruses/isolation & purification , Adolescent , Adult , Aged , Aged, 80 and over , Child , Child, Preschool , Female , Genome, Viral , High-Throughput Nucleotide Sequencing , Humans , Infant , Infant, Newborn , Kuwait/epidemiology , Male , Metagenomics , Middle Aged , Multiplex Polymerase Chain Reaction , RNA, Viral/genetics , Real-Time Polymerase Chain Reaction , Respiratory Tract Infections/epidemiology , Viruses/classification , Young Adult
10.
Microorganisms ; 12(2)2024 Jan 24.
Article in English | MEDLINE | ID: mdl-38399651

ABSTRACT

BACKGROUND: Eukaryotes' whole-genome sequencing is crucial for species identification, gene detection, and protein annotation. Oxford Nanopore Technology (ONT) is an affordable and rapid platform for sequencing eukaryotes; however, the relatively higher error rates require computational and bioinformatic efforts to produce more accurate genome assemblies. Here, we evaluated the effect of read correction tools on eukaryote genome completeness, gene detection and protein annotation. METHODS: Reads generated by ONT of four eukaryotes, C. albicans, C. gattii, S. cerevisiae, and P. falciparum, were assembled using minimap2 and underwent three rounds of read correction using flye, medaka and racon. The generates consensus FASTA files were compared for total length (bp), genome completeness, gene detection, and protein-annotation by QUAST, BUSCO, BRAKER1 and InterProScan, respectively. RESULTS: Genome completeness was dependent on the assembly method rather than on the read correction tool; however, medaka performed better than flye and racon. Racon significantly performed better than flye and medaka in gene detection, while both racon and medaka significantly performed better than flye in protein-annotation. CONCLUSION: We show that three rounds of read correction significantly affect gene detection and protein annotation, which are dependent on assembly quality in preference to assembly completeness.

11.
Vaccines (Basel) ; 12(10)2024 Sep 27.
Article in English | MEDLINE | ID: mdl-39460273

ABSTRACT

Staphylococcus aureus (SA) is a major bacterial pathogen and causes a wide range of clinical infections in humans leading to severe outcomes including meningitis, endocarditis, and sepsis. This literature review examines studies on host immune responses after infections with SA and methicillin-resistant Staphylococcus aureus (MRSA) and their immune evasion mechanisms. Furthermore, information about vaccines and immunotherapies against SA and MRSA is reviewed. We found promising toxoid vaccine approaches, which deserve further research. We also found support for antitoxin therapies and immunomodulating therapies as high-potential research areas. Although many promising vaccines and immunotherapy candidates have been studied in animal models, more human clinical studies are needed to confirm their long-term safety and efficacy.

12.
Article in English | MEDLINE | ID: mdl-39200594

ABSTRACT

Antimicrobial resistance (AMR) has emerged as a conspicuous global public health threat. The World Health Organization (WHO) has launched the "One-Health" approach, which encourages the assessment of antibiotic resistance genes (ARGs) within an environment to constrain and alleviate the development of AMR. The prolonged use and overuse of antibiotics in treating human and veterinary illnesses, and the inability of wastewater treatment plants to remove them have resulted in elevated concentrations of these metabolites in the surroundings. Microbes residing within these settings acquire resistance under selective pressure and circulate between the air-land interface. Initial evidence on the indoor environments of wastewater treatment plants, hospitals, and livestock-rearing facilities as channels of AMR has been documented. Long- and short-range transport in a downwind direction disseminate aerosols within urban communities. Inhalation of such aerosols poses a considerable occupational and public health risk. The horizontal gene transfer (HGT) is another plausible route of AMR spread. The characterization of ARGs in the atmosphere therefore calls for cutting-edge research. In the present review, we provide a succinct summary of the studies that demonstrated aerosols as a media of AMR transport in the atmosphere, strengthening the need to biomonitor these pernicious pollutants. This review will be a useful resource for environmental researchers, healthcare practitioners, and policymakers to issue related health advisories.


Subject(s)
Aerosols , Gene Transfer, Horizontal , Aerosols/analysis , Humans , Biological Monitoring , Drug Resistance, Microbial/genetics , Air Microbiology , Air Pollution, Indoor/analysis , Environmental Monitoring , Anti-Bacterial Agents/analysis , Drug Resistance, Bacterial/genetics
13.
Med Princ Pract ; 22 Suppl 1: 43-51, 2013.
Article in English | MEDLINE | ID: mdl-24008694

ABSTRACT

Comparative analyses of the Mycobacterium tuberculosis genome with the genomes of other mycobacteria have led to the identification of several genomic regions of difference (RDs) between M. tuberculosis and M. bovis BCG. The identification of immunodominant and HLA-promiscuous antigens and peptides encoded by these RDs could be useful for diagnosis and the development of new vaccines against tuberculosis. The analysis of RD proteins and peptides by in silico methods (using computational programs to predict major and HLA-promiscuous antigenic proteins and peptides) and experimental validations (using peripheral blood mononuclear cells and sera from tuberculosis patients and BCG-vaccinated healthy subjects to assess antigen-specific cellular and humoral immune responses in vitro) identified several major antigens and peptides. To evaluate the in vivo potentials, the genes of immunodominant antigens were cloned and expressed in DNA vaccine vectors. Immunizations of experimental animals with the recombinant constructs induced antigen-specific cellular responses. Further experiments showed that each of these proteins had several T and B cell epitopes scattered throughout their sequence, which confirmed their strong immunogenicity. In conclusion, the bioinformatics-based in silico identification of promiscuous antigens and peptides of M. tuberculosis is a useful approach to identify new candidates important for diagnosis and vaccine applications.


Subject(s)
Mycobacterium tuberculosis/genetics , Tuberculosis Vaccines/genetics , Tuberculosis/genetics , Tuberculosis/prevention & control , Antigens, Bacterial/genetics , Bacterial Proteins/genetics , Genes, Bacterial , HLA Antigens/genetics , Humans , Leukocytes, Mononuclear/immunology , Peptides/genetics , Tuberculin Test , Tuberculosis/diagnosis
14.
PLoS One ; 18(10): e0292828, 2023.
Article in English | MEDLINE | ID: mdl-37812595

ABSTRACT

[This corrects the article DOI: 10.1371/journal.pone.0260314.].

15.
Diagnostics (Basel) ; 13(8)2023 Apr 21.
Article in English | MEDLINE | ID: mdl-37189605

ABSTRACT

Increasing numbers of neonates with serious bacterial infections, due to resistant bacteria, are associated with considerable morbidity and mortality rates. The aim of this study was to evaluate the prevalence of drug-resistant Enterobacteriaceae in the neonatal population and their mothers in Farwaniya Hospital in Kuwait and to determine the basis of resistance. Rectal screening swabs were taken from 242 mothers and 242 neonates in labor rooms and wards. Identification and sensitivity testing were performed using the VITEK® 2 system. Each isolate flagged with any resistance was subjected to the E-test susceptibility method. The detection of resistance genes was performed by PCR, and the Sanger sequencing method was used to identify mutations. Among 168 samples tested by the E-test method, no MDR Enterobacteriaceae were detected among the neonates, while 12 (13.6%) isolates from the mothers' samples were MDR. ESBL, aminoglycosides, fluoroquinolones, and folate pathway inhibitor resistance genes were detected, while beta-lactam-beta-lactamase inhibitor combinations, carbapenems, and tigecycline resistance genes were not. Our results showed that the prevalence of antibiotic resistance in Enterobacteriaceae obtained from neonates in Kuwait is low, and this is encouraging. Furthermore, it is possible to conclude that neonates are acquiring resistance mostly from the environment and after birth but not from their mothers.

16.
Vaccines (Basel) ; 11(11)2023 Oct 25.
Article in English | MEDLINE | ID: mdl-38005965

ABSTRACT

Cancer immunotherapies refer to the concept of retraining the immune system to target malignant cells. Multiple immunotherapeutic options exist including immune modulating antibodies, immune stimulating cytokines, chimeric antigen receptor T cell therapy, and vaccines. Overall, this field has advanced rapidly as knowledge of the tumor microenvironment, immunological pathways, and biotechnology expands. Specifically, advancements in neoantigen identification, characterization, and formulation into a vaccine show promise. This review is focused on previously United States Food and Drug Administration-approved cancer therapeutic vaccines and neoantigen-based vaccine developments along with the associated relevant clinical trials.

17.
Exp Clin Cardiol ; 17(3): 95-100, 2012 Sep.
Article in English | MEDLINE | ID: mdl-23620695

ABSTRACT

BACKGROUND: The protective effects of 17-beta estradiol (E2) on cardiac tissue during ischemia/reperfusion (I/R) injury have not yet been fully elucidated. OBJECTIVE: To assess the protective effects of short- and long-term E2 treatments on cardiac tissue exposed to I/R, and to assess the effects of these treatments in combination with ischemic preconditioning (IPC) on cardiac protection from I/R injury. METHODS: SPRAGUE DAWLEY RATS WERE ASSIGNED TO THE FOLLOWING TREATMENT PROTOCOLS: control (no preconditioning); IPC (isolated hearts were subjected to two cycles of 5 min global ischemia followed by 10 min of reperfusion); E2 preconditioning (E2PC; isolated hearts were subjected to E2 pharmacological perfusion for 15 min); short-term in vivo E2 pretreatment for 3 h; long-term in vivo E2 pretreatment or withdrawal (ovariectomy followed by a six-week treatment with E2 or a placebo); combined IPC and E2PC; combined IPC and short- or long-term E2 pretreatments or withdrawal. All hearts were isolated and stabilized for at least 30 min before being subjected to 40 min of global ischemia followed by 30 min of reperfusion; left ventricular function and vascular hemodynamics were then assessed. RESULTS: IPC, E2PC and short-term E2 pretreatment led to the recovery of left ventricle function and vascular hemodynamics. Long-term E2 and placebo treatments did not result in any protection compared with untreated controls. The combination of E2PC or short-term E2 treatments with IPC did not block the IPC protection or result in any additional protection to the heart. Long-term E2 treatment blocked IPC protection; however, placebo treatment did not. CONCLUSIONS: Short-term treatment with E2 protected the heart against I/R injury through a pathway involving the regulation of tumour necrosis factor-alpha. The combination of short-term E2 treatment with IPC did not provide additional protection to the heart. Short-term E2 treatment may be a suitable alternative for classical estrogen replacement therapy.

18.
Int J Mycobacteriol ; 11(1): 10-15, 2022.
Article in English | MEDLINE | ID: mdl-35295018

ABSTRACT

Background: Early secreted antigenic target of 6 kDa (ESAT6) is low-molecular-weight and immunodominant protein of Mycobacterium tuberculosis with relevance to diagnosis and vaccine development. Analysis of the M. tuberculosis genome has shown the existence of 23 ESAT6-like genes. This study was aimed to determine M. tuberculosis-specificity vis-à-vis crossreactivity of ESAT6-like genes and encoded proteins and their potential in the diagnosis and vaccine development. Methods: All ESAT6-like proteins were characterized using the webserver Tuberculist. The sequence identities were determined using basic local alignment search tool. Results: The genes for six ESAT6-like proteins were located in M. tuberculosis-specific genomic regions of differences (RDs), i.e., EsxA and EsxB in RD1, EsxO and EsxP in RD7, and EsxV and EsxW in RD9. The genes for other ESAT6-like proteins were located in the genomic regions shared with other mycobacteria. Based on sequence identities, the ESA6-like proteins were divided into four subfamilies of 15 proteins and no subfamily of 8 proteins. The members of subfamilies 1-4 shared extensive sequence identities among the members of each subfamily. Each member of subfamily 1 (EsxI, EsxL, EsxN, EsxO, EsxV) and subfamily 2 (EsxJ, EsxK, EsxM, EsxP, EsxW) were homologs. Hence, the gene sequences identical to EsxO and EsxP located in RD7, and EsxV and EsxW located in RD9 were also present in the regions of M. tuberculosis genome shared with other mycobacteria. Conclusion: Because of their specificity to M. tuberculosis, only EsxA (ESAT6) and EsxB (CFP10) will be useful in the specific diagnosis. However, other ESAT6-like proteins may be useful for vaccine development against tuberculosis.


Subject(s)
Mycobacterium tuberculosis , Tuberculosis, Lymph Node , Vaccines , Antigens, Bacterial/genetics , Bacterial Proteins/metabolism , Humans , Vaccines/metabolism
19.
Mol Genet Genomic Med ; 10(5): e1930, 2022 05.
Article in English | MEDLINE | ID: mdl-35349224

ABSTRACT

BACKGROUND: Vitamin D-binding protein or group-specific component (Gc) is the major plasma carrier protein of Vitamin D. Two single nucleotide polymorphisms, rs7041 (NM_000583.3:c.1296G>T;NP_000574.2:p.Asp432Glu) and rs4588 (c.1307C>A; p.Thr436Lys), in the GC gene result in three major genotypes, that is, GC1F (c.1296T, c.1307C), GC1S (c.1296G, c.1307C), GC2 (c.1296T, c.1307A), and phenotypes such as Gc1F (p.432Asp, p.436Thr), Gc1S (p.432Glu, p.436Thr), and Gc2 (p.432Asp, p.436Lys). Significant variations in the frequencies of GC subtypes (genotypes/phenotypes) are reported in different populations living in different geographical locations, for example, GC1S/Gc1S (c.1296G, c.1307C/p.432Glu, p.436Thr) and GC2/Gc2 (c.1296T, c.1307A/p.432Asp, p.436Lys) are predominant in Caucasians and people living in the northern hemisphere, and GC1F/Gc1F (c.1296T, c.1307C/p.432Asp, p.436Thr) is predominant in Africans. However, frequencies of major GC subtypes are not known in the Kuwaiti population. In this study, we investigated 512 alleles to identify the major GC subtypes in Kuwaiti nationals. METHODS: Genomic DNA was isolated from blood samples of 128 healthy subjects. DNA regions covering the targeted mutations were amplified by PCR. Amplified DNAs were sequenced by the Sanger method and analyzed for specific mutations to determine the GC genotypes and phenotypes. RESULTS: The results identified the presence of four GC genotypes/phenotypes namely GC1F/Gc1F (c.1296T, c.1307C/p.432Asp, p.436Thr), GC1S/Gc1S (c.1296G, c.1307C/p.432Glu, p.436Thr), GC2/Gc2 (c.1296T, c.1307A/p.432Asp, p.436Lys), and GC3/Gc3 (c.1296G;c.1307A/p.432Glu, p.436Lys). Among the allelic subtypes (n = 512), GC1S (c.1296G; c.1307C) (n = 270, 52.7%) was predominant, followed by GC1F (c.1296T; c.1307C) (n = 138, 27%), GC2 (c.1296T; c.1307A) (n = 72, 14%), and GC3 (c.1296G; c.1307A) (n = 32, 6.3%). Three common subtypes, that is, GC1F (c.1296T; c.1307C), GC1S (c.1296G; c.1307C), and GC2 (c.1296T; c.1307A) are well documented in the literature, but GC3 (c.1296T; c.1307A) is an uncommon variant found in our study subjects. CONCLUSION: We found that GC subtype distribution was unique in the Kuwaiti population, with some affinity to Caucasians. Several factors including ancestral origin, migration history, and environmental forces such as solar intensity may be responsible for the unique distribution of GC subtypes in this population.


Subject(s)
Vitamin D-Binding Protein , Alleles , Blood Proteins/genetics , Humans , Kuwait , Polymorphism, Single Nucleotide , Vitamin D/metabolism , Vitamin D-Binding Protein/genetics
20.
Vaccines (Basel) ; 10(8)2022 Jul 29.
Article in English | MEDLINE | ID: mdl-36016096

ABSTRACT

Messenger RNA has been studied by everyone, from vaccine developers to high school biology students, since the discovery of its isolation in 1961 [...].

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