scholarly journals Sprouts as functional food- an approach towards the identification of natural antibiotic resistance breakers

2019 ◽  
Vol 9 (1-s) ◽  
pp. 23-35
Author(s):  
Valli. S Abiraami ◽  
S. Uma Gowrie
Keyword(s):  
Antibiotic Resistance ◽  
Bioactive Compounds ◽  
Bacterial Infections ◽  
Shigella Flexneri ◽  
Health Concern ◽  
Human Pathogens ◽  
Topoisomerase Iv ◽  
In Silico Docking ◽  
Horse Gram ◽  
Macrotyloma Uniflorum

Antibiotics are medicines used to prevent and treat bacterial infections. Antibiotic resistance occurs when bacteria change in response to the use of these medicines. Investigation studies related to discovery of novel antibiotics to deal with antibacterial resistance from natural edible food products have been one of the significant research interests in recent years. The main objective of the study is to identify the bioactive compounds having the natural antibiotic resistance breaking property, by giving scientific validation to the existing bioactive compounds present in the sprouts and recommending the horse gram and mixed sprouts as a natural dietary supplement, a measure for the management of the disease, Shigellosis. Qualitative screening of the phytoconstituents (using different solvent extracts) and quantitative analysis of the primary and secondary phytoconstituents were carried out in methanol and aqueous extracts of the horse gram and mixed sprouts (fresh and dried) using standard protocols in two different samples- horse gram sprouts (Macrotyloma uniflorum (Lam.) Verdc.) and mixed sprouts of combination (Cicer arietinum L. (Chick pea), Macrotyloma uniflorum (Lam.) Verdc. (horse gram) and Vigna radiata (L.). Antibacterial activity of both the samples against human pathogens namely Staphylococcus aureus, Escherichia coli, Salmonella typhi, Klebsiella pneumoniae and Shigella flexneri were studied. In horse gram and mixed sprouts, maximum zone of inhibitions were shown by Shigella flexneri, a food and water borne pathogen leading to outbreaks of Shigellosis, a major public health concern. Ciprofloxacin is a broad spectrum of antimicrobial carboxyfluoroquinolones. The bactericidal action of Ciprofloxacin is by inhibiting DNA gyrase, a type II topoisomerase and topoisomerase IV, which are required for bacterial DNA replication. Phytochemical characterization (FTIR and GC-MS) and antibacterial studies proved the presence of essential phytoconstituents like terpenoids, fatty acids, proteins, carbohydrates and vitamins. Several bioactive compounds obtained from GC-MS analysis were screened for Ciprofloxacin antibiotic resistance. The specific phytoconstituents, DL-Proline from horse gram sprouts and Geranyl geraniol from mixed sprouts was tend to act as novel antibiotic resistance breakers which was proved through in silico docking.   

scholarly journals Coexistence of Antibiotic Resistance Genes and Virulence Factors Deciphered by Large-Scale Complete Genome Analysis

mSystems ◽  
2020 ◽  
Vol 5 (3) ◽  
Author(s):  
Yu Pan ◽  
Jiaxiong Zeng ◽  
Liguan Li ◽  
Jintao Yang ◽  
Ziyun Tang ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Virulence Factors ◽  
Resistance Genes ◽  
Large Scale ◽  
Antibiotic Resistance Genes ◽  
Comprehensive Analysis ◽  
Health Concern ◽  
Human Pathogens ◽  
Bacterial Genomes ◽  
Gene Acquisition

ABSTRACT Widespread use of antibiotics has enhanced the evolution of highly resilient pathogens and poses a severe risk to human health via coselection of antibiotic resistance genes (ARGs) and virulence factors (VFs). In this study, we rigorously evaluate the abundance relationship and physical linkage between ARGs and VFs by performing a comprehensive analysis of 9,070 bacterial genomes isolated from multiple species and hosts. The coexistence of ARGs and VFs was observed in bacteria across distinct phyla, pathogenicities, and habitats, especially among human-associated pathogens. The coexistence patterns of gene elements in different habitats and pathogenicity groups were similar, presumably due to frequent gene transfer. A shorter intergenic distance between mobile genetic elements and ARGs/VFs was detected in human/animal-associated bacteria, indicating a higher transfer potential. Increased accumulation of exogenous ARGs/VFs in human pathogens highlights the importance of gene acquisition in the evolution of human commensal bacteria. Overall, the findings provide insights into the genic features of combinations of ARG-VF and expand our understanding of ARG-VF coexistence in bacteria. IMPORTANCE Antibiotic resistance has become a serious global health concern. Despite numerous case studies, a comprehensive analysis of ARG and VF coexistence in bacteria is lacking. In this study, we explore the coexistence profiles of ARGs and VFs in diverse categories of bacteria by using a high-resolution bioinformatics approach. We also provide compelling evidence of unique ARG-VF gene pairs coexisting in specific bacterial genomes and reveal the potential risk associated with the coexistence of ARGs and VFs in organisms in both clinical settings and environments.

scholarly journals Investigating colistin drug resistance: The role of high-throughput sequencing and bioinformatics

F1000Research ◽  
2019 ◽  
Vol 8 ◽  
pp. 150 ◽  
Author(s):  
Dickson Aruhomukama ◽  
Ivan Sserwadda ◽  
Gerald Mboowa
Keyword(s):  
Antibiotic Resistance ◽  
High Throughput ◽  
Bacterial Infections ◽  
High Throughput Sequencing ◽  
Health Concern ◽  
Gram Negative Bacteria ◽  
Drug Resistant ◽  
Colistin Resistance ◽  
Gram Negative

Bacterial infections involving antibiotic resistant gram-negative bacteria continue to increase and represent a major global public health concern. Resistance to antibiotics in these bacteria is mediated by chromosomal and/or acquired resistance mechanisms, these give rise to multi-drug resistant (MDR) or extensive drug resistant (XDR) bacterial strains. Most recently, a novel acquired plasmid mediated resistance mechanism to colistin, an antibiotic that had been set apart as the last resort antibiotic in the treatment of infections involving MDR and XDR gram-negative bacteria, has been reported. Plasmid mediated colistin resistant gram-negative bacteria have been described to be pan-drug resistant, implying a state devoid of alternative antibiotic therapeutic options. This review describes the evolution of antibiotic resistance to plasmid mediated colistin resistance, and discusses the potential role of high-throughput sequencing technologies, genomics and bioinformatics towards improving antibiotic resistance surveillance, the search for novel drug targets and precision antibiotic therapy focused at combating colistin resistance, and antimicrobial resistance as a whole.

scholarly journals Factors favouring the evolution of multidrug resistance in bacteria

2020 ◽  
Vol 17 (168) ◽  
pp. 20200105
Author(s):  
Eliott Jacopin ◽  
Sonja Lehtinen ◽  
Florence Débarre ◽  
François Blanquart
Keyword(s):  
Antibiotic Resistance ◽  
Multidrug Resistance ◽  
Bacterial Infections ◽  
Large Fraction ◽  
Bacterial Species ◽  
Geographical Location ◽  
Host Population ◽  
Commensal Bacteria ◽  
Health Concern ◽  
Multiple Drugs

The evolution of multidrug antibiotic resistance in commensal bacteria is an important public health concern. Commensal bacteria such as Escherichia coli , Streptococcus pneumoniae or Staphylococcus aureus , are also opportunistic pathogens causing a large fraction of the community-acquired and hospital-acquired bacterial infections. Multidrug resistance (MDR) makes these infections harder to treat with antibiotics and may thus cause substantial additional morbidity and mortality. Here, we develop an evolutionary epidemiology model to identify the factors favouring the evolution of MDR in commensal bacteria. The model describes the evolution of antibiotic resistance in a commensal bacterial species evolving in a host population subjected to multiple antibiotic treatments. We combine statistical analysis of a large number of simulations and mathematical analysis to understand the model behaviour. We find that MDR evolves more readily when it is less costly than expected from the combinations of single resistances (positive epistasis). MDR frequently evolves when bacteria are in contact with multiple drugs prescribed in the host population, even if individual hosts are only treated with a single drug at a time. MDR is favoured when the host population is structured in different classes that vary in their rates of antibiotic treatment. However, under most circumstances, recombination between loci involved in resistance does not meaningfully affect the equilibrium frequency of MDR. Together, these results suggest that MDR is a frequent evolutionary outcome in commensal bacteria that encounter the variety of antibiotics prescribed in the host population. A better characterization of the variability in antibiotic use across the host population (e.g. across age classes or geographical location) would help predict which MDR genotypes will most readily evolve.

Bioactive Compounds of Horse Gram (Macrotyloma uniflorum Lam. [Verdc.])

2020 ◽  
pp. 1-39
Author(s):  
Krishnananda Pralhad Ingle ◽  
Jameel M. Al-Khayri ◽  
Pritha Chakraborty ◽  
Gopal Wasudeo Narkhede ◽  
Penna Suprasanna
Keyword(s):  
Bioactive Compounds ◽  
Horse Gram ◽  
Macrotyloma Uniflorum

Bioactive Compounds of Horse Gram (Macrotyloma uniflorum Lam. [Verdc.])

2021 ◽  
pp. 583-621
Author(s):  
Krishnananda Pralhad Ingle ◽  
Jameel M. Al-Khayri ◽  
Pritha Chakraborty ◽  
Gopal Wasudeo Narkhede ◽  
Penna Suprasanna
Keyword(s):  
Bioactive Compounds ◽  
Horse Gram ◽  
Macrotyloma Uniflorum

scholarly journals Rapid resistome mapping using nanopore sequencing

2016 ◽  
Author(s):  
Eric van der Helm ◽  
Lejla Imamovic ◽  
Mostafa M Hashim Ellabaan ◽  
Willem van Schaik ◽  
Anna Koza ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Antibiotic Treatment ◽  
Bacterial Infections ◽  
Antibiotic Resistance Genes ◽  
Modern Medicine ◽  
Nanopore Sequencing ◽  
Human Pathogens ◽  
Major Threat ◽  
Gene Acquisition ◽  
Collateral Effects

AbstractThe emergence of antibiotic resistance in human pathogens has become a major threat to modern medicine and in particular hospitalized patients. The outcome of antibiotic treatment can be affected by the composition of the gut resistome either by enabling resistance gene acquisition of infecting pathogens or by modulating the collateral effects of antibiotic treatment on the commensal microbiome. Accordingly, knowledge of the gut resistome composition could enable more effective and individualized treatment of bacterial infections. Yet, rapid workflows for resistome characterization are lacking. To address this challenge we developed the poreFUME workflow that deploys functional metagenomic selections and nanopore sequencing to resistome mapping. We demonstrate the approach by functionally characterizing the gut resistome of an ICU patient. The accuracy of the poreFUME pipeline is >97 % sufficient for the reliable annotation of antibiotic resistance genes. The poreFUME pipeline provides a promising approach for efficient resistome profiling that could inform antibiotic treatment decisions in the future.

scholarly journals Predicting drug targets by homology modelling of Pseudomonas aeruginosa proteins of unknown function

PLoS ONE ◽  
2021 ◽  
Vol 16 (10) ◽  
pp. e0258385
Author(s):  
Nikolina Babic ◽  
Filip Kovacic
Keyword(s):  
Antibiotic Resistance ◽  
Unknown Function ◽  
Drug Targets ◽  
Bacterial Infections ◽  
Homology Modelling ◽  
Functional Characterization ◽  
Host Recognition ◽  
Large Set ◽  
Human Pathogens ◽  
Hypothetical Genes

The efficacy of antibiotics to treat bacterial infections declines rapidly due to antibiotic resistance. This problem has stimulated the development of novel antibiotics, but most attempts have failed. Consequently, the idea of mining uncharacterized genes of pathogens to identify potential targets for entirely new classes of antibiotics was proposed. Without knowing the biochemical function of a protein, it is difficult to validate its potential for drug targeting; therefore, the functional characterization of bacterial proteins of unknown function must be accelerated. Here, we present a paradigm for comprehensively predicting the biochemical functions of a large set of proteins encoded by hypothetical genes in human pathogens to identify candidate drug targets. A high-throughput approach based on homology modelling with ten templates per target protein was applied to the set of 2103 P. aeruginosa proteins encoded by hypothetical genes. The >21000 homology modelling results obtained and available biological and biochemical information about several thousand templates were scrutinized to predict the function of reliably modelled proteins of unknown function. This approach resulted in assigning one or often multiple putative functions to hundreds of enzymes, ligand-binding proteins and transporters. New biochemical functions were predicted for 41 proteins whose essential or virulence-related roles in P. aeruginosa were already experimentally demonstrated. Eleven of them were shortlisted as promising drug targets that participate in essential pathways (maintaining genome and cell wall integrity), virulence-related processes (adhesion, cell motility, host recognition) or antibiotic resistance, which are general drug targets. These proteins are conserved in other WHO priority pathogens but not in humans; therefore, they represent high-potential targets for preclinical studies. These and many more biochemical functions assigned to uncharacterized proteins of P. aeruginosa, made available as PaPUF database, may guide the design of experimental screening of inhibitors, which is a crucial step towards the validation of the highest-potential targets for the development of novel drugs against P. aeruginosa and other high-priority pathogens.

scholarly journals Determination of antibiotic resistance patterns of Vibrio parahaemolyticus from shrimp and shellfish in Selangor, Malaysia

2019 ◽  
Vol 2 (1) ◽  
Author(s):  
Vengadesh Letchumanan ◽  
Nurul-Syakima Ab Mutalib ◽  
Sunny Hei Wong ◽  
Kok-Gan Chan ◽  
Learn-Han Lee
Keyword(s):  
Antibiotic Resistance ◽  
Vibrio Parahaemolyticus ◽  
Bacterial Infections ◽  
Pathogenic Bacteria ◽  
Large Scale ◽  
Health Concern ◽  
Resistance Pattern ◽  
Resistant Bacteria ◽  
Resistance Patterns ◽  
Plasmid Profiling

High consumer demand for seafood has led to the need for large-scale, reliable supply through aquaculture farming. However, bacterial infections - which can spread rapidly among the dense farming area pose a major threat to this industry. The farmers therefore often resort to extensive use of antibiotics, both prophylactically and therapeutically, in order to protect their stocks. The extensive use of antibiotics in aquaculture has been postulated to represent a major contributing factor in the rising incidence of antimicrobial resistant pathogenic bacteria in seafood; which may then lead to the spread of antimicrobial resistant bacteria in the environment as well as posing a significant threat to human health. This study aimed to characterize antibiotic resistance of Vibrio parahaemolyticus from shrimp and shellfish in Selangor, Malaysia. The antibiotic susceptibility of 385 V. parahaemolyticus isolates was investigated against 14 antibiotics followed by plasmid profiling and plasmid curing to determine the antibiotic mediation. A large number of isolates showed resistance to ampicillin (85%), amikacin (66.8%), and kanamycin (50.1%). A notable resistance pattern was also observed to the third generation cephalosporins (cefotaxime 55.8% and ceftazidime 34%). Only 338 V. parahaemolyticus isolates had 1-7 different plasmids and could be categorized into 27 patterns based on the number and pattern of plasmid present. Interestingly, there was no correlation between the number of plasmids and antibiotic resistant patterns seen in the isolates. The antibiotic resistance was mediated by both chromosomal and plasmid mediation among the resistant isolates. In summary, our results demonstrate that incidence of pathogenic V. parahaemolyticus in seafood in Selangor remains in relatively assuring levels, however the identification of antibiotic resistance among the isolates does rises a public health concern and warrants for continuous surveillance.

scholarly journals Predicting drug targets by homology modelling of Pseudomonas aeruginosa proteins of unknown function

2021 ◽  
Author(s):  
Nikolina Babic ◽  
Filip Kovacic
Keyword(s):  
Antibiotic Resistance ◽  
Unknown Function ◽  
Drug Targets ◽  
Bacterial Infections ◽  
Homology Modelling ◽  
Host Recognition ◽  
Large Set ◽  
Human Pathogens ◽  
Functional Characterisation ◽  
Hypothetical Genes

Efficacies of antibiotics to treat bacterial infections rapidly decline due to antibiotic resistance. This stimulated the development of novel antibiotics, but most attempts failed. As a response, the idea of mining uncharacterised genes of pathogens to identify potential targets for entirely new classes of antibiotics raised. Without knowing the biochemical function of a protein it is difficult to validate its potential for drug targeting; therefore progress in the functional characterisation of bacterial proteins of an unknown function must be accelerated. Here we present a paradigm for comprehensively predicting biochemical functions of a large set of proteins encoded by hypothetical genes in human pathogens, to identify candidate drug targets. A high-throughput approach based on homology modelling with ten templates per target protein was applied on the set of 2103 P. aeruginosa proteins encoded by hypothetical genes. Obtained >21000 homology modelling results and available biological and biochemical information about several thousand templates was scrutinised to predict the function of reliably modelled proteins of unknown function. This approach resulted in assigning, one or often multiple, putative functions to hundreds of enzymes, ligand-binding proteins and transporters. New biochemical functions were predicted for 41 proteins whose essential or virulence-related roles in P. aeruginosa were already experimentally demonstrated. Eleven of them were shortlisted as promising drug targets which participate in essential pathways (maintaining genome and cell wall integrity), virulence-related processes (adhesion, cell motility, host recognition) or antibiotic resistance, which are general drug targets. These proteins are conserved among other WHO priority pathogens but not in humans, therefore they represent high-potential targets for pre-clinical studies. These and many more biochemical functions assigned to uncharacterised proteins of P. aeruginosa, available as PaPUF database may guide the design of experimental screening of inhibitors which is a crucial step toward validation of the most potential targets for the development of novel drugs against P. aeruginosa and other high-priority pathogens.

scholarly journals Investigating colistin drug resistance: The role of high-throughput sequencing and bioinformatics

F1000Research ◽  
2019 ◽  
Vol 8 ◽  
pp. 150 ◽  
Author(s):  
Dickson Aruhomukama ◽  
Ivan Sserwadda ◽  
Gerald Mboowa
Keyword(s):  
Antibiotic Resistance ◽  
High Throughput ◽  
Bacterial Infections ◽  
High Throughput Sequencing ◽  
Health Concern ◽  
Gram Negative Bacteria ◽  
Drug Resistant ◽  
Colistin Resistance ◽  
Gram Negative

Bacterial infections involving antibiotic-resistant gram-negative bacteria continue to increase and represent a major global public health concern. Resistance to antibiotics in these bacteria is mediated by chromosomal and/or acquired resistance mechanisms, these give rise to multi-drug resistant (MDR), extensive-drug resistant (XDR) or pan-drug resistant (PDR) bacterial strains. Most recently, plasmid-mediated resistance to colistin, an antibiotic that had been set apart as the last resort antibiotic in the treatment of infections involving MDR, XDR and PDR gram-negative bacteria has been reported. Plasmid-mediated colistin resistant gram-negative bacteria have been described to be PDR, implying a state devoid of alternative antibiotic therapeutic options. This review concisely describes the evolution of antibiotic resistance to plasmid-mediated colistin resistance and discusses the potential role of high-throughput sequencing technologies, genomics, and bioinformatics towards improving antibiotic resistance surveillance, the search for novel drug targets and precision antibiotic therapy focused at combating colistin resistance, and antibiotic resistance as a whole.

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