scholarly journals Metagenomic Profiling and Identification of Antimicrobial Resistance Genes from Airborne Microbial Communities

2015 ◽  
Vol 7 (1) ◽  
Author(s):  
Tamar Dickerson ◽  
Jonathan L. Jacobs ◽  
Nicole Waybright ◽  
Danielle Swales ◽  
Peggy Lowary ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Antimicrobial Resistance ◽  
Microbial Communities ◽  
Bacterial Communities ◽  
Temporal Dynamics ◽  
Animal Health ◽  
Functional Metagenomics ◽  
Antimicrobial Resistance Genes ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Antimicrobial resistance (AMR) is recognized as a severe threat to human and animal health worldwide, yet relatively little is known regarding the bioavailability of AMR genes in airborne microbial communities. Hence, the objective of our study is to use next generation sequencing (NGS) to assess the temporal dynamics of airborne bacterial communities as well as functional metagenomics to investigate the dispersion of AMR genes present within them.

scholarly journals Microbiome and Antimicrobial Resistance Gene Dynamics in International Travelers

2018 ◽  
Author(s):  
Charles Langelier ◽  
Michael Graves ◽  
Katrina Kalantar ◽  
Saharai Caldera ◽  
Robert Durrant ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Antimicrobial Resistance ◽  
Gut Microbiota ◽  
Microbial Communities ◽  
Resistance Gene ◽  
Resistance Genes ◽  
Antimicrobial Resistance Genes ◽  
Antimicrobial Resistance Gene ◽  
Global Exchange ◽  
Generation Sequencing

AbstractWe engaged metagenomic next generation sequencing to longitudinally assess the gut microbiota and antimicrobial resistomes of international travelers to understand global exchange of resistant organisms. Travel resulted in an increase in antimicrobial resistance genes and a greater proportion of Escherichia species within gut microbial communities without impacting diversity.

scholarly journals Metagenomic Analysis of the Gut Bacteriome of Usherhopper, Poekilocerus bufonius (Klug) from Hadda, Saudi Arabia

2021 ◽  
Author(s):  
Nabih A. Baeshen ◽  
Mazen A. Majeed ◽  
Mohammed Abdullah T Alotaibi ◽  
Mohamed Hamed Alnefai ◽  
Aala A. Abulfaraj ◽  
...  
Keyword(s):  
Saudi Arabia ◽  
Next Generation Sequencing ◽  
Pest Management ◽  
Bacterial Communities ◽  
The Other ◽  
Economic Losses ◽  
Plant Fibers ◽  
Next Generation Sequencing Ngs ◽  
Effective Conservation ◽  
Generation Sequencing

Abstract Background:Microbial communities that colonize insect guts contribute positively to the absorption of nutrients, immunity and the overall health of the host. Recent studies have been tapered towards only economically important arthropods, particularly honeybees. On the other hand, arthropods such as grasshoppers are considered as pests because they create havoc leading to economic losses. Grasshoppers are considered phytophagous pests that have a large appetite for plant fibers, whose digestion depend largely on the bacterial communities in their guts. This study characterises the gut microbiome in Usherhopper, Poekilocerus bufonius using the metagenomics methods through the next generation sequencing (NGS). Results:A total of 59,072,222 bacterial reads were recorded which were classified into phylum and genus levels. Proteobacteria were the most shared at the phylum-level whereas Wolbachia were the most dominant genera based on the total reads. Conclusions: The host-microbiome interactions and their perceived influence on the ecosystem are yet to be fully explained, therefore a detailed study is pivotal in order to enforce effective conservation and pest management.

scholarly journals The challenges of designing a benchmark strategy for bioinformatics pipelines in the identification of antimicrobial resistance determinants using next generation sequencing technologies

F1000Research ◽  
2018 ◽  
Vol 7 ◽  
pp. 459 ◽  
Author(s):  
Alexandre Angers-Loustau ◽  
Mauro Petrillo ◽  
Johan Bengtsson-Palme ◽  
Thomas Berendonk ◽  
Burton Blais ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Antimicrobial Resistance ◽  
One Health ◽  
Next Generation ◽  
Sequencing Technologies ◽  
Novel Technology ◽  
Molecular Determinants ◽  
Next Generation Sequencing Ngs ◽  
Proper Interpretation ◽  
Generation Sequencing

Next-Generation Sequencing (NGS) technologies are expected to play a crucial role in the surveillance of infectious diseases, with their unprecedented capabilities for the characterisation of genetic information underlying the virulence and antimicrobial resistance (AMR) properties of microorganisms.  In the implementation of any novel technology for regulatory purposes, important considerations such as harmonisation, validation and quality assurance need to be addressed.  NGS technologies pose unique challenges in these regards, in part due to their reliance on bioinformatics for the processing and proper interpretation of the data produced.  Well-designed benchmark resources are thus needed to evaluate, validate and ensure continued quality control over the bioinformatics component of the process.  This concept was explored as part of a workshop on "Next-generation sequencing technologies and antimicrobial resistance" held October 4-5 2017.   Challenges involved in the development of such a benchmark resource, with a specific focus on identifying the molecular determinants of AMR, were identified. For each of the challenges, sets of unsolved questions that will need to be tackled for them to be properly addressed were compiled. These take into consideration the requirement for monitoring of AMR bacteria in humans, animals, food and the environment, which is aligned with the principles of a “One Health” approach.

scholarly journals Next generation sequencing for pathogen detection in periprosthetic joint infections

2021 ◽  
Vol 6 (4) ◽  
pp. 236-244
Author(s):  
Pier F. Indelli ◽  
Stefano Ghirardelli ◽  
Bruno Violante ◽  
Derek F. Amanatullah
Keyword(s):  
Next Generation Sequencing ◽  
Antimicrobial Resistance ◽  
Pathogen Detection ◽  
High Sensitivity ◽  
Diagnostic Tools ◽  
Next Generation ◽  
Comprehensive Collection ◽  
Joint Infections ◽  
Antimicrobial Resistance Genes ◽  
Generation Sequencing

Periprosthetic joint infections (PJI) represent one of the most catastrophic complications following total joint arthroplasty (TJA). The lack of standardized diagnostic tests and protocols for PJI is a challenge for arthroplasty surgeons. Next generation sequencing (NGS) is an innovative diagnostic tool that can sequence microbial deoxyribonucleic acids (DNA) from a synovial fluid sample: all DNA present in a specimen is sequenced in parallel, generating millions of reads. It has been shown to be extremely useful in a culture-negative PJI setting. Metagenomic NGS (mNGS) allows for universal pathogen detection, regardless of microbe type, in a 24–48-hour timeframe: in its nanopore-base variation, mNGS also allows for antimicrobial resistance characterization. Cell-free DNA (cfDNA) NGS, characterized by lack of the cell lysis step, has a fast run-time (hours) and, together with a high sensitivity and specificity in microorganism isolation, may provide information on the presence of antimicrobial resistance genes. Metagenomics and cfDNA testing have reduced the time needed to detect infecting bacteria and represent very promising technologies for fast PJI diagnosis. NGS technologies are revolutionary methods that could disrupt the diagnostic paradigm of PJI, but a comprehensive collection of clinical evidence is still needed before they become widely used diagnostic tools. Cite this article: EFORT Open Rev 2021;6:236-244. DOI: 10.1302/2058-5241.6.200099

scholarly journals Comparison of bacterial communities in roots of selected trees with and without summer truffle (Tuber aestivum) ectomycorrhiza

2021 ◽  
Vol 63 (2) ◽  
pp. 97-111
Author(s):  
Marta Siebyła ◽  
Iwona Szyp-Borowska
Keyword(s):  
Next Generation Sequencing ◽  
Bacterial Communities ◽  
Bacterial Species ◽  
Tuber Aestivum ◽  
Bacterial Composition ◽  
Next Generation Sequencing Ngs ◽  
And Control ◽  
Sanger Method ◽  
Generation Sequencing ◽  
Control Samples

Abstract In this study, we examined the effect of the presence of mycorrhiza and ascomata of summer truffle (Tuber aestivum) on the bacterial composition of roots from small trees growing in selected sites of the Nida Basin. Qualitative DNA sequencing methods such as Sanger and next-generation sequencing (NGS) were used. The Sanger method revealed different bacterial species compositions between the samples where summer truffle ascomata was recorded and control samples. Five genera of bacteria could be distinguished: Bacillus, Erwinia, Pseudomonas, Rahnella and Serratia, among which the most numerous were Pseudomonas (Gammmaproteobacteria class) at 32.9%. The results obtained by the NGS method also showed differences in species composition of the bacteria depending on the study sample. Seven genera of bacteria were distinguished: Rhizorhabdus, Methylotenera, Sphingomonas, Nitrosospira, Streptomyces, Methyloceanibacter and Niastella, which dominated in roots from the truffle sites. Telmatobacter, Roseiarcus, Granulicella, Paludibaculum, Acidipila, Acidisphaera and Aliidongia dominated in roots from the control sites. With the NGS method, it is possible to identify the microbiome of a whole root, while only a root fragment can be analysed by the Sanger method. These results extend the scope of knowledge on the preferences of certain groups of bacteria associated with truffles and their influence on the formation of ascomata in summer truffles. Our results may also be useful in selecting and monitoring sites that promote ascomata of Tuber aestivum.

scholarly journals The challenges of designing a benchmark strategy for bioinformatics pipelines in the identification of antimicrobial resistance determinants using next generation sequencing technologies

F1000Research ◽  
2018 ◽  
Vol 7 ◽  
pp. 459 ◽  
Author(s):  
Alexandre Angers-Loustau ◽  
Mauro Petrillo ◽  
Johan Bengtsson-Palme ◽  
Thomas Berendonk ◽  
Burton Blais ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Antimicrobial Resistance ◽  
One Health ◽  
Next Generation ◽  
Sequencing Technologies ◽  
Novel Technology ◽  
Molecular Determinants ◽  
Next Generation Sequencing Ngs ◽  
Proper Interpretation ◽  
Generation Sequencing

Next-Generation Sequencing (NGS) technologies are expected to play a crucial role in the surveillance of infectious diseases, with their unprecedented capabilities for the characterisation of genetic information underlying the virulence and antimicrobial resistance (AMR) properties of microorganisms.  In the implementation of any novel technology for regulatory purposes, important considerations such as harmonisation, validation and quality assurance need to be addressed.  NGS technologies pose unique challenges in these regards, in part due to their reliance on bioinformatics for the processing and proper interpretation of the data produced.  Well-designed benchmark resources are thus needed to evaluate, validate and ensure continued quality control over the bioinformatics component of the process.  This concept was explored as part of a workshop on "Next-generation sequencing technologies and antimicrobial resistance" held October 4-5 2017.   Challenges involved in the development of such a benchmark resource, with a specific focus on identifying the molecular determinants of AMR, were identified. For each of the challenges, sets of unsolved questions that will need to be tackled for them to be properly addressed were compiled. These take into consideration the requirement for monitoring of AMR bacteria in humans, animals, food and the environment, which is aligned with the principles of a “One Health” approach.

scholarly journals Trends in bacterial and fungal communities in ant nests observed with Terminal-Restriction Fragment Length Polymorphism (T-RFLP) and Next Generation Sequencing (NGS) techniques—validity and compatibility in ecological studies

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5289 ◽  
Author(s):  
Stafva Lindström ◽  
Owen Rowe ◽  
Sari Timonen ◽  
Liselotte Sundström ◽  
Helena Johansson
Keyword(s):  
Next Generation Sequencing ◽  
Restriction Fragment Length Polymorphism ◽  
Microbial Communities ◽  
Length Polymorphism ◽  
Fragment Length Polymorphism ◽  
Illumina Miseq ◽  
Fungal Communities ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing ◽  
Restriction Fragment Length

Microbes are ubiquitous and often occur in functionally and taxonomically complex communities. Unveiling these community dynamics is one of the main challenges of microbial research. Combining a robust, cost effective and widely used method such as Terminal Restriction Fragment Length Polymorphism (T-RFLP) with a Next Generation Sequencing (NGS) method (Illumina MiSeq), offers a solid alternative for comprehensive assessment of microbial communities. Here, these two methods were combined in a study of complex bacterial and fungal communities in the nest mounds of the antFormica exsecta, with the aim to assess the degree to which these methods can be used to complement each other. The results show that these methodologies capture similar spatiotemporal variations, as well as corresponding functional and taxonomical detail, of the microbial communities in a challenging medium consisting of soil, decomposing plant litter and an insect inhabitant. Both methods are suitable for the analysis of complex environmental microbial communities, but when combined, they complement each other well and can provide even more robust results. T-RFLP can be trusted to show similar general community patterns as Illumina MiSeq and remains a good option if resources for NGS methods are lacking.

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