Metagenomics Next Generation Sequencing (mNGS): An Exciting Tool for Early and Accurate Diagnosing Plant Fungal Pathogens

Gökdemir, F. Şeyma; İşeri, Özlem Darcansoy; Sharma, Abhıshek; Achar, P. N.; Eyidoğan, Füsun

doi:10.20944/preprints202208.0457.v1

Cited by 4 publications

(3 citation statements)

References 24 publications

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“…Additionally, our study highlights another advantage of mNGS, which is its ability to directly target specific NTM strains without the need for further strain typing. This feature saves time and cost while enabling clinicians to guide precise dosing decisions for NTM infections (Gopalaswamy et al, 2020) (Gökdemir et al, 2022). By providing information on the specific NTM strain, mNGS facilitates tailored antibiotic treatment, which can lead to improved patient outcomes.…”

Section: Pcr Testing Resultsmentioning

confidence: 99%

“…This unbiased approach is particularly valuable for the early diagnosis of difficultto-detect infections. Consequently, mNGS is increasingly being employed in clinical practice, playing a significant role in improving diagnostic capabilities (Li et al, 2021;Gökdemir et al, 2022). However, the diagnostic potential and specificity of mNGS in NTM diagnosis are still being evaluated in clinical practice.…”

Section: Introductionmentioning

confidence: 99%

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Metagenomic next-generation sequencing assistance in identifying non-tuberculous mycobacterial infections

Wang,

Xing

2023

Front. Cell. Infect. Microbiol.

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IntroductionThe advent of metagenomics next-generation sequencing (mNGS) has garnered attention as a novel method for detecting pathogenic infections, including Non-Tuberculous Mycobacterial (NTM) and tuberculosis (TB).However, the robustness and specificity of mNGS in NTM diagnostics have not been fully explored.MethodsIn this retrospective study, we enrolled 27 patients with NTM genomic sequences via mNGS and conducted a comprehensive clinical evaluation.ResultsPulmonary NTM disease was the most commonly observed presentation, with a subset of patients also presenting with extrapulmonary NTM infections.mNGS analysis identified six distinct NTM species, primarily Mycobacteriumavium complex (MAC), followed by Mycobacterium intracellulare andMycobacterium abscessus. Conventional routine culture methods encountered challenges, resulting in negative results for all available 22 samples. Among the 10 patients who underwent quantitative polymerase chain reaction (qPCR) testing, five tested positive for NTM.DiscussionIt is important to note that further species typing is necessary to determine the specific NTM type, as traditional pathogen detection methods serve as an initial step. In contrast, when supplemented with pathogen data, enables the identification of specific species, facilitating precise treatment decisions. In conclusion, mNGS demonstrates significant potential in aidingthe diagnosis of NTMdisease by rapidly detecting NTM pathogens and guiding treatment strategies. Its enhanced performance, faster turnaround time (TAT), and species identification capabilities make mNGS a promising tool for managing NTM infections.

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Section: Pcr Testing Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Metagenomic next-generation sequencing assistance in identifying non-tuberculous mycobacterial infections

Wang,

Xing

2023

Front. Cell. Infect. Microbiol.

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“…Despite decades of medical and technological advances, therapies targeting the gut flora for critical illnesses have not been developed on a large scale. Metagenomics next generation sequencing (mNGS) is a new method of high-throughput RNA/DNA sequencing that enables the detection of all pathogenic bacteria in a sample without bias (Diao et al, 2022;Gökdemir et al, 2022). This method allows further exploration of the composition, diversity, gene function, and drug resistance genes of the gut microbiota.…”

Section: Introductionmentioning

confidence: 99%

Pediatric intensive care unit treatment alters the diversity and composition of the gut microbiota and antimicrobial resistance gene expression in critically ill children

Xu,

Kong,

et al. 2023

Front. Microbiol.

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IntroductionCommon critical illnesses are a growing economic burden on healthcare worldwide. However, therapies targeting the gut microbiota for critical illnesses have not been developed on a large scale. This study aimed to investigate the changes in the characteristics of the gut microbiota in critically ill children after short-term pediatric intensive care unit (PICU) treatments.MethodsAnal swab samples were prospectively collected from March 2021 to March 2022 from children admitted to the PICU of Xinhua Hospital who received broad-spectrum antibiotics on days 1 (the D1 group) and 7 (the D7 group) of the PICU treatment. The structural and functional characteristics of the gut microbiota of critically ill children were explored using metagenomic next-generation sequencing (mNGS) technology, and a comparative analysis of samples from D1 and D7 was conducted.ResultsAfter 7 days of PICU admission, a significant decrease was noted in the richness of the gut microbiota in critically ill children, while the bacterial diversity and the community structure between groups remained stable to some extent. The relative abundance of Bacilli and Lactobacillales was significantly higher, and that of Campylobacter hominis was significantly lower in the D7 group than in the D1 group. The random forest model revealed that Prevotella coporis and Enterobacter cloacae were bacterial biomarkers between groups. LEfSe revealed that two Gene Ontology entries, GO:0071555 (cell wall organization) and GO:005508 (transmembrane transport), changed significantly after the short-term treatment in the PICU. In addition, 30 KEGG pathways were mainly related to the activity of enzymes and proteins during the processes of metabolism, DNA catabolism and repair, and substance transport. Finally, 31 antimicrobial resistance genes had significantly different levels between the D7 and D1 groups. The top 10 up-regulated genes were Erm(A), ErmX, LptD, eptB, SAT-4, tetO, adeJ, adeF, APH(3′)-IIIa, and tetM.ConclusionThe composition, gene function, and resistance genes of gut microbiota of critically ill children can change significantly after short PICU treatments. Our findings provide a substantial basis for a better understanding of the structure and function of gut microbiota and their role in critical illnesses.

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The Role of Fungi in Food Production and Processing

Pouris,

Kolyva,

Bratakou

et al. 2024

Applied Sciences

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Fungi play an important and multifaceted role in the production and processing of food, influencing various stages from cultivation to consumption. This paper explores the complex relationship between fungi and food systems, highlighting their diverse contributions. Firstly, fungi serve as essential agents in food cultivation, aiding in the breakdown of organic matter and the recycling of nutrients, and promoting plant growth through symbiotic relationships. Moreover, fungi such as yeasts and molds are integral to fermentation processes, yielding a wide array of fermented foods and beverages with unique flavors and textures. Additionally, fungi are indispensable in the creation of enzymes and bioactive compounds utilized in food processing, enhancing the nutritional value, shelf life, and safety. However, certain fungal species pose significant challenges as food spoilage agents and mycotoxin producers, necessitating stringent quality control measures. Understanding the intricate interplay between fungi and food systems is essential for optimizing food production, ensuring food security, and mitigating the risks associated with fungal contamination. This paper synthesizes current research to elucidate the important role that fungus play in shaping the modern food industry and underscores the importance of ongoing scientific inquiry in harnessing their potential for sustainable and safe food production.

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Metagenomics Next Generation Sequencing (mNGS): An Exciting Tool for Early and Accurate Diagnosing Plant Fungal Pathogens

Cited by 4 publications

References 24 publications

Metagenomic next-generation sequencing assistance in identifying non-tuberculous mycobacterial infections

Metagenomic next-generation sequencing assistance in identifying non-tuberculous mycobacterial infections

Pediatric intensive care unit treatment alters the diversity and composition of the gut microbiota and antimicrobial resistance gene expression in critically ill children

The Role of Fungi in Food Production and Processing

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