Draft genome sequence of the extended-spectrum -lactamase-producing escherichia coli isolate INF13/18/A, recovered from Kelantan, Malaysia

We describe here the draft genome sequence and basic characteristics of Escherichia coli isolate INF13/18/A, which was isolated from Universiti Sains Malaysia (USM) Hospital. This isolate was identified as an extended-spectrum -lactamaseproducing Escherichia coli strain harboring the antimicrobial resistance genes TEM, CTX-M-1, and CTX-M-9

In silico prediction of cell wall remodeling genes in tomato, banana, melon and grape

Ripening is a complex developmental process and involves many events such as textural and constitutional changes. The texture of fleshy fruits is one of the major criteria for consumer choice. However, the molecular determinants of ripening- associated changes in texture or “softening” are relatively poorly understood and seem to involve a large number of cell wall remodelling factors. The recent completion of the tomato genome sequence has revealed more than 50 cell wall structure-related genes that are expressed during fruit development and ripening and may impact texture changes in this fruit. The aim of the project is to compare, on a genome-wide scale, ripening-related gene expression in a range of fleshy fruits and especially those linked with cell wall remodelling via computer simulation. Then by identifying orthologous genes in different fruit species to make predictions about those genes likely to important for the softening process in all fleshy fruits. Comparative genomics analysis of tomato (Solanum lycopersicum), banana (Musa acuminate), melon (Cucumis melo) and grape (Vitis vinifera), has been undertaken using Inparanoid, Multiparanoid and BLAST2GO software. This analysis showed that a total of 8,982 (25.86%) gene models could be identified in common between all four genomes based on comparison of amino acid sequences. Of these genes, 262 in tomato, 252 in grape, 261 in melon, and 198 in banana were identified as encoding cell wall structure-related proteins. However, comparison of the expression patterns of these genes revealed that most were expressed in tissues other than ripening fruits, and of the fruit expressed genes only a small number were common between different fruit species. This in silico analysis should provide additional clues as a target for manipulation of fruit softening in a range of fleshy fruit species. These also provide new opportunities to develop varieties of tomatoes that can survive the trip from the farm to the grocery store whilst maintaining excellent flavour and shelf-life

Whole genome sequencing analysis of salmonella enterica serovar typhi: history and current approaches

In recent years, the advance in whole-genome sequencing technology has changed the study of infectious diseases. The emergence of genome sequencing has improved the understanding of infectious diseases, which has revamped many fields, such as molecular microbiology, epidemiology, infection control, and vaccine production. In this review we discuss the findings of Salmonella enterica serovar Typhi genomes, publicly accessible from the initial complete genome to the recent update of Salmonella enterica serovar Typhi genomes, which has greatly improved Salmonella enterica serovar Typhi and other pathogen genomic research. Significant information on genetic changes, evolution, antimicrobial resistance, virulence, pathogenesis, and investigation from the genome sequencing of S. Typhi is also addressed. This review will gather information on the variation of the Salmonella enterica serovar Typhi genomes and hopefully facilitate our understanding of their genome evolution, dynamics of adaptation, and pathogenesis for the development of the typhoid point-of-care diagnostics, medications, and vaccines

In silico analysis and 3d structure prediction of putative UDP-Glycosyltransfer-ase 76G1 protein in stevia Rebaudiana MS007

Stevia rebaudiana is a plant of the Asteraceae family that is used as a natural sweet-ener. Stevia has been shown to be safe for human consumption and has been utilised as a sweetener substitute for diabetic and obese people. In this study, the structure and gene content involved in the synthesis of putative UDP-glycosyltransferase 76G1 (UGT76G1) protein in S. rebaudiana MS007 were analysed using an in-silico method. Homologous search using BlastP revealed the highest percentage of identity, score, and E-value for UDP-glycosyltransferase 76G1-like of Helianthus annuus (ID: XP_021973845.1). The presence of IPR002213 UDP-glucuronosyl/UDP-glucosyl-transferase entry, which is available at locations 89bp to 246 bp, was also verified by the protein family search using InterPro. MEGA-X software was used to construct a molecular phylogeny study, revealing that this protein belongs to the Asteraceae fam-ily. To predict the primary, secondary, and tertiary protein structures of the putative UGT76G1 protein, the ProtParam, ExPasy, PSIPRED, and Phyre2 programmes were implemented. The putative UGT76G1 protein’s tertiary structure prediction was given a score of 100.0% confidence by the single highest scoring template and a coverage of 98%, with the dimension of the model being (Å) of X: 52.453, Y: 61.270, and Z: 48.102. The UGT76G1 model fulfilled the quality standards and was approved for further analysis after validation performed by PROCHECK, VERIFY3D, and ER-RAT. Thus, the findings of this work have contributed to a better knowledge of puta-tive UDP-glycosyltransferase 76G1 features and target recognition processes, which will lead to better information on protein-protein interaction in S. rebaudiana MS007

Near-Infrared Spectroscopy as a Potential COVID-19 Early Detection Method: A Review and Future Perspective

The coronavirus disease 2019 (COVID-19) pandemic is a worldwide health anxiety. The rapid dispersion of the infection globally results in unparalleled economic, social, and health impacts. The pathogen that causes COVID-19 is known as a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). A fast and low-cost diagnosis method for COVID-19 disease can play an important role in controlling its proliferation. Near-infrared spectroscopy (NIRS) is a quick, non-destructive, non-invasive, and inexpensive technique for profiling the chemical and physical structures of a wide range of samples. Furthermore, the NIRS has the advantage of incorporating the internet of things (IoT) application for the effective control and treatment of the disease. In recent years, a significant advancement in instrumentation and spectral analysis methods has resulted in a remarkable impact on the NIRS applications, especially in the medical discipline. To date, NIRS has been applied as a technique for detecting various viruses including zika (ZIKV), chikungunya (CHIKV), influenza, hepatitis C, dengue (DENV), and human immunodeficiency (HIV). This review aims to outline some historical and contemporary applications of NIRS in virology and its merit as a novel diagnostic technique for SARS-CoV-2

In Silico analysis and 3D structure prediction of putative UDP-Glycosyltransferase 76G1 protein in Stevia rebaudiana MS007

Stevia rebaudiana is a plant of the Asteraceae family that is used as a natural sweetener. Stevia has been shown to be safe for human consumption and has been utilised as a sweetener substitute for diabetic and obese people. In this study, the structure and gene content involved in the synthesis of putative UDP-glycosyltransferase 76G1 (UGT76G1) protein in S. rebaudiana MS007 were analysed using an in-silico method. Homologous search using BlastP revealed the highest percentage of identity, score, and E-value for UDP-glycosyltransferase 76G1-like of Helianthus annuus (ID:XP_021973845.1). The presence of IPR002213 UDP-glucuronosyl/UDP-glucosyltransferase entry, which is available at locations 89bp to 246 bp, was also verified by the protein family search using InterPro. MEGA-X software was used to construct a molecular phylogeny study, revealing that this protein belongs to the Asteraceae family. To predict the primary, secondary, and tertiary protein structures of the putative UGT76G1 protein, the ProtParam, ExPasy, PSIPRED, and Phyre2 programmes were implemented. The putative UGT76G1 protein’s tertiary structure prediction was given a score of 100.0% confidence by the single highest scoring template and a coverage of 98%, with the dimension of the model being (Å) of X: 52.453, Y: 61.270, and Z: 48.102. The UGT76G1 model fulfilled the quality standards and was approved for further analysis after validation performed by PROCHECK, VERIFY3D, and ERRAT. Thus, the findings of this work have contributed to a better knowledge of putative UDP-glycosyltransferase 76G1 features and target recognition processes, which will lead to better information on protein-protein interaction in S. rebaudiana MS007

Antimicrobial resistance in methicillin-resistant staphylococcus aureus

In the medical community, antibiotics are revered as a miracle because they stop diseases brought on by pathogenic bacteria. Antibiotics have become the cornerstone of contemporary medical advancements ever since penicillin was discovered. Antibiotic resistance developed among germs quickly, placing a strain in the medical field. Methicillin-resistant Staphylococcus aureus (MRSA), Since 1961, has emerged as the major general antimicrobial resistant bacteria (AMR) worldwide. MRSA can easily transmit across the hospital system and has mostly gained resistance to medications called beta-lactamases. This enzyme destroys the cell wall of beta-lactam antibiotics resulting in resistance against that respective antibiotic. Daptomycin, linezolid and vancomycin were previously used to treat MRSA infections. However, due to mutations and Single nucleotide polymorphisms (SNPs) in Open reading frames (ORFs) and SCCmec machinery of respective antibody, MRSA developed resistance against those antibiotics. The MRSA strains (USA300, CC398, CC130 etc.), when their pan-genomes were analyzed were found the genes involved in invoking resistance against the antibiotics as well as the epidemiology of that respective strain. PENC (penicillin plus potassium clavulanate) is the new antibiotic showing potential in treatment of MRSA though it is itself resistant against penicillin alone. In this review, our main focus is on mechanism of development of AMR in MRSA, how different ORFs are involved in evoking resistance in MRSA and what is the core-genome of different antimicrobial resistant MRSA

Colorimetric Approach for Nucleic Acid Salmonella spp. Detection: A Systematic Review

Water- and food-related health issues have received a lot of attention recently because food-poisoning bacteria, in particular, are becoming serious threats to human health. Currently, techniques used to detect these bacteria are time-consuming and laborious. To overcome these challenges, the colorimetric strategy is attractive because it provides simple, rapid and accurate sensing for the detection of Salmonella spp. bacteria. The aim of this study is to review the progress regarding the colorimetric method of nucleic acid for Salmonella detection. A literature search was conducted using three databases (PubMed, Scopus and ScienceDirect). Of the 88 studies identified in our search, 15 were included for further analysis. Salmonella bacteria from different species, such as S. Typhimurium, S. Enteritidis, S. Typhi and S. Paratyphi A, were identified using the colorimetric method. The limit of detection (LoD) was evaluated in two types of concentrations, which were colony-forming unit (CFU) and CFU per mL. The majority of the studies used spiked samples (53%) rather than real samples (33%) to determine the LoDs. More research is needed to assess the sensitivity and specificity of colorimetric nucleic acid in bacterial detection, as well as its potential use in routine diagnosis

Updates on Epstein–Barr Virus (EBV)-Associated Nasopharyngeal Carcinoma: Emphasis on the Latent Gene Products of EBV

Nasopharyngeal carcinoma (NPC) is an uncommon type of malignancy/cancer worldwide. However, NPC is an endemic disease in southeast Asia and southern China and the reasons behind the underlying for such changes are unclear. Even though the Epstein–Barr infection (EBV) has been suggested as an important reason for undistinguishable NPC, the EBV itself is not adequate to source this type of cancer. The risk factors, for example, genetic susceptibility, and environmental factors might be associated with EBV to undertake a part in the NPC carcinogenesis. Normal healthy people have a memory B cell pool where the EBV persists, and any disturbance of this connection leads to virus-associated B cell malignancies. Less is known about the relationship between EBV and epithelial cell tumors, especially the EBV-associated nasopharyngeal carcinoma (EBVaNPC) and EBV-associated gastric carcinoma (EBVaGC). Currently, it is believed that premalignant genetic changes in epithelial cells contribute to the aberrant establishment of viral latency in these tumors. The early and late phases of NPC patients’ survival rates vary significantly. The presence of EBV in all tumor cells presents prospects for the development of innovative therapeutic and diagnostic techniques, despite the fact that the virus’s exact involvement in the carcinogenic process is presently not very well known. EBV research continues to shed light on the carcinogenic process, which is important for a more comprehensive knowledge of tumor etiology and the development of targeted cancer therapeutics. In order to screen for NPC, EBV-related biomarkers have been widely used in a few high-incidence locations because of their close associations with the risks of NPC. The current review highlights the scientific importance of EBV and its possible association with NPC

Global Prevalence of Nosocomial Multidrug-Resistant Klebsiella pneumoniae: A Systematic Review and Meta-Analysis

The emergence of nosocomial multidrug-resistant Klebsiella pneumoniae is an escalating public health threat worldwide. The prevalence of nosocomial infections due to K. pneumoniae was recorded up to 10%. In this systematic review and meta-analysis, which were conducted according to the guidelines of Preferred Reporting Items for Systematic Review and Meta-Analysis, 1092 articles were screened from four databases of which 47 studies fulfilled the selected criteria. By performing a random-effect model, the pooled prevalence of nosocomial multidrug-resistant K. pneumoniae was estimated at 32.8% (95% CI, 23.6–43.6), with high heterogeneity (I2 98.29%, p-value < 0.001). The estimated prevalence of this pathogen and a few related studies were discussed, raising awareness of the spread of multidrug-resistant K. pneumoniae in the healthcare setting. The emergence of nosocomial multidrug-resistant K. pneumoniae is expected to increase globally in the future, and the best treatments for treating and preventing this pathogen should be acknowledged by healthcare staff