Evaluation of a new antimicrobial agent production (RSMM C3) by using metagenomics approaches from Egyptian marine biota

Shaaban, Mohamed T.; Abdelhamid, Reham M; Zayed, Muhammad; Ali, Safaa M.

doi:10.1016/j.btre.2022.e00706

Cited by 5 publications

(5 citation statements)

References 41 publications

(38 reference statements)

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“…Furthermore, it was further confirmed using an analytical profile index (API) [ 28 ]. Additionally, the bacterial DNA was isolated for molecular identification using DNeasy® Blood & Tissue Kit [ 29 , 30 ]. The quality of extracted DNA was evaluated by Agarose gel electrophoresis [ 31 ], and the concentration was estimated by nanodrop.…”

Section: Methodsmentioning

confidence: 99%

Microbiological and molecular studies on a multidrug-resistant Pseudomonas aeruginosa from a liver transplant patient with urinary tract infection in Egypt

Shaaban,

Abdel-Raouf,

Zayed

et al. 2024

BMC Microbiol

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Background Pseudomonas aeruginosa is an opportunistic pathogen responsible for complicated UTIs and exhibits high antibiotic resistance, leading to increased mortality rates, especially in cases of multidrug-resistant strains. This study aimed to investigate the antibiotic susceptibility patterns and genomic characterization of XDR strains identified in end-stage liver disease patients who underwent liver transplants. Methods In this study, a number of 30 individuals who underwent liver transplants were registered. Ninety urine and 60 wound site swab samples were collected and processed for culturing, identification, and antimicrobial sensitivity. Extensively drug-resistant strain EMARA01 was confirmed through Sanger sequencing and was then processed for whole genome sequencing to characterize the genomic pattern. Sequencing data were processed for de novo assembly using various tools and databases, including genome annotation, serotype identification, virulence factor genes, and antimicrobial resistance gene. Pangenome analysis of randomly selected 147 reference strains and EMAR01 sequenced strain was performed using the Bacterial Pan Genome Analysis (BPGA) software. Results Of these total examined samples, nosocomial infection due to P. aeruginosa was detected in twelve patients’ samples. AST analysis showed that P. aeruginosa strains exhibit resistance to tobramycin, erythromycin, and gentamicin, followed by piperacillin and ofloxacin, and no strains exhibit resistance to meropenem and imipenem. The CARD database identified 59 AMR genes similar to the EMAR01 strain genome and mostly belong to the family involved in the resistance-nodulation-cell division (RND) antibiotic efflux pump. Five genes; nalC, nalD, MexR, MexA, and MexB, exhibit resistance to 14 classes of antibiotics, while two AMR; CpxR, and OprM, exhibit resistance to 15 classes of drugs. Pangenome analysis revealed that the pan-genome remained open, suggesting the potential for acquiring accessory and unique genes. Notably, the genes predominantly involved in amino acid transport metabolism were identified using the KEGG database. Conclusions This study provides valuable insights into the antimicrobial resistance profile, genetic features, and genomic evolution of P. aeruginosa strains causing UTIs in liver transplant patients. The findings emphasize the significance of comprehending AMR mechanisms and genetic diversity in P. aeruginosa for developing effective treatment strategies and infection control measures.

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Section: Methodsmentioning

confidence: 99%

Microbiological and molecular studies on a multidrug-resistant Pseudomonas aeruginosa from a liver transplant patient with urinary tract infection in Egypt

Shaaban,

Abdel-Raouf,

Zayed

et al. 2024

BMC Microbiol

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“…Omics data can support the conservation of ecosystems and the sustainable use of marine resources (for example Bowser et al, 2020;Turunen et al, 2021), as well as the monitoring of wild animal populations such as fish (Andruszkiewicz et al, 2017) or mammals (Suarez-Bregua et al, 2022). In addition, omics data can be integrated into ecosystem models to develop innovative investigations in food security (for example Grützke et al, 2019;Sequino et al, 2022), biodiscovery (for example Mahapatra et al, 2020;Shaaban et al, 2022), novel treatments in biofuels (Sartaj et al, 2022) and bioremediation (Rodrıǵuez et al, 2022), and other services such as disease detection in the environment (Wurtzer et al, 2022) or clinical diagnostics (Forbes et al, 2017). In the last decade, omics methods have matured into viable solutions to support efficient biodiversity observation from microbes to whales, reorienting our understanding of ecology and evolution, as well as the ways humans are embedded in the physical world (Canonico et al, 2019;Rodrıǵuez-Ezpeleta et al, 2021).…”

Section: The Role Of Omics In Marine Biological Observationmentioning

confidence: 99%

European marine omics biodiversity observation network: a strategic outline for the implementation of omics approaches in ocean observation

Santi,

Beluche,

Beraud

et al. 2023

Front. Mar. Sci.

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Marine ecosystems, ranging from coastal seas and wetlands to the open ocean, accommodate a wealth of biological diversity from small microorganisms to large mammals. This biodiversity and its associated ecosystem function occurs across complex spatial and temporal scales and is not yet fully understood. Given the wide range of external pressures on the marine environment, this knowledge is crucial for enabling effective conservation measures and defining the limits of sustainable use. The development and application of omics-based approaches to biodiversity research has helped overcome hurdles, such as allowing the previously hidden community of microbial life to be identified, thereby enabling a holistic view of an entire ecosystem’s biodiversity and functioning. The potential of omics-based approaches for marine ecosystems observation is enormous and their added value to ecosystem monitoring, management, and conservation is widely acknowledged. Despite these encouraging prospects, most omics-based studies are short-termed and typically cover only small spatial scales which therefore fail to include the full spatio-temporal complexity and dynamics of the system. To date, few attempts have been made to establish standardised, coordinated, broad scaled, and long-term omics observation networks. Here we outline the creation of an omics-based marine observation network at the European scale, the European Marine Omics Biodiversity Observation Network (EMO BON). We illustrate how linking multiple existing individual observation efforts increases the observational power in large-scale assessments of status and change in biodiversity in the oceans. Such large-scale observation efforts have the added value of cross-border cooperation, are characterised by shared costs through economies of scale, and produce structured, comparable data. The key components required to compile reference environmental datasets and how these should be linked are major challenges that we address.

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“…1 Mega7 software was used to 10.3389/fmicb.2023.1180463 Frontiers in Microbiology 03 frontiersin.org accomplish molecular phylogeny and multiple sequence alignment present in the database (NCBI). A neighbor-joining (NJ) tree and a maximum parsimony (MP) tree using bootstrapping were made using this alignment (Hassan et al, 2018;Shaaban et al, 2022).…”

Section: Phylogenetic Analysismentioning

confidence: 99%

Characterization of an isolated lactase enzyme produced by Bacillus licheniformis ALSZ2 as a potential pharmaceutical supplement for lactose intolerance

Amin,

Olama,

Ali

2023

Front. Microbiol.

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IntroductionLactose intolerance is a widespread problem that affects people of many different races all over the world. The following pharmacological supplements can improve the lives of those who suffer from this issue.MethodsThis work focused on lactase producer isolation and statistical design (Plackett–Burman, and BOX–Behnken) to maximize the effectiveness of environmental factors. A lactase-producing bacterium was chosen from a discovery of 100 strains in soil that had previously been polluted with dairy products. Plackett-Burman investigated fifteen variables.ResultsThe most critical variables that lead to increased lactase synthesis are glucose, peptone, and magnesium sulfate (MgSO4). The ideal process conditions for the creation of lactase yield among the stated variables were then determined using a BOX-Benken design. To establish a polynomial quadratic relationship between the three variables and lactase activity, the Box–Behnken design level was used. The EXCEL-solver nonlinear optimization technique was used to predict the best form for lactase production. The ideal temperature and pH levels have been determined, both before and after the lactase purification process, to achieve the highest performance of isolated lactase.ConclusionAccording to this study, Bacillus licheniformis is a perfect supply of the lactase enzyme (β -Galactosidase), It can be used as a product to assist people who have health issues due to lactose intolerance.

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Evaluation of a new antimicrobial agent production (RSMM C3) by using metagenomics approaches from Egyptian marine biota

Cited by 5 publications

References 41 publications

Microbiological and molecular studies on a multidrug-resistant Pseudomonas aeruginosa from a liver transplant patient with urinary tract infection in Egypt

Microbiological and molecular studies on a multidrug-resistant Pseudomonas aeruginosa from a liver transplant patient with urinary tract infection in Egypt

European marine omics biodiversity observation network: a strategic outline for the implementation of omics approaches in ocean observation

Characterization of an isolated lactase enzyme produced by Bacillus licheniformis ALSZ2 as a potential pharmaceutical supplement for lactose intolerance

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