scholarly journals Translating Lung Microbiome Profiles into the Next-Generation Diagnostic Gold Standard for Pneumonia: a Clinical Investigator’s Perspective

mSystems ◽  
2018 ◽  
Vol 3 (2) ◽  
Author(s):  
Georgios D. Kitsios
Keyword(s):  
Pulmonary Infections ◽  
Next Generation ◽  
Clinical Validity ◽  
Lung Microbiome ◽  
Current State ◽  
Incubation Periods ◽  
Culture Independent ◽  
Diagnostic Approaches ◽  
Microbial Dna ◽  
Generation Sequencing

ABSTRACT Severe bacterial pneumonia is a major global cause of morbidity and mortality, yet current diagnostic approaches rely on identification of causative pathogens by cultures, which require extended incubation periods and often fail to detect relevant pathogens. Consequently, patients are prescribed broad-spectrum antibiotics in a “one-size-fits-all” manner, which may be inappropriate for their individual needs and promote antibiotic resistance. My research focuses on leveraging next-generation sequencing of microbial DNA directly from patient samples for the development of new, culture-independent definitions of pneumonia. In this perspective article, I discuss the current state of the field and focus on the conceptual and research design challenges for clinical translation. With ongoing technological advancements and application of computational biology methods for assessing clinical validity and utility, I anticipate that sequencing-based diagnostics will soon be able to positively disrupt the way we think about, diagnose, and treat pulmonary infections.

scholarly journals Recent advances in understanding the ecology of the lung microbiota and deciphering the gut-lung axis

2020 ◽  
Vol 319 (4) ◽  
pp. L710-L716 ◽  
Author(s):  
Kent A. Willis ◽  
Justin D. Stewart ◽  
Namasivayam Ambalavanan
Keyword(s):  
Next Generation Sequencing ◽  
Ecological Perspective ◽  
Next Generation ◽  
Sequencing Technologies ◽  
Lung Microbiome ◽  
Recent Advances ◽  
Organ Systems ◽  
Culture Independent ◽  
Microbiome Research ◽  
Generation Sequencing

A rapidly expanding new field of lung research has been produced by the emergence of culture-independent next-generation sequencing technologies. While pulmonary microbiome research lags behind the exploration of the microbiome in other organ systems, the field is maturing and has recently produced multiple exciting discoveries. In this mini-review, we will explore recent advances in our understanding of the lung microbiome and the gut-lung axis from an ecological perspective.

MICROBIOMA: AMIGO O ENEMIGO EN PACIENTES CON COVID - 19

SCIENTIARVM ◽  
2015 ◽  
Vol 1 (1) ◽  
pp. 15-21
Author(s):  
Katherine Milagros Quispe Medina ◽  
◽  
Angel Sixto Mamani Ruelas ◽  
Brenda Jasmin Alvarez Vera ◽  
Yasmin Yessenia Silvestre Gutierrez ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Gastrointestinal Tract ◽  
Molecular Biology ◽  
Gut Microbiome ◽  
Next Generation ◽  
Multiple Factors ◽  
Lung Microbiome ◽  
The Relationship ◽  
Generation Sequencing ◽  
Clinical Cases

The research of the microbiome concerning various diseases has grown in the last ten years due to the advances in molecular biology and next-generation sequencing, finding interactions with various pathologies. The new coronavirus 19 (SARS-COV 2) pandemic has aroused interest in the study of multiple factors that could influence in the development of symptoms mainly due to the interaction of the microbiome whether of the respiratory or gastrointestinal tract finally in the prognosis. Therefore, in this study, we focus on reviewing and analyzing the current bibliography of research and clinical cases about the relationship between the lung and gut microbiome and COVID-19, highlighting its effect on infected patients, aiming to contribute to this new line of research. Keywords: Microbiome, COVID-19, SARS-COV 2, gut microbiome, lung microbiome.

scholarly journals The integration of emerging omics approaches to advance precision medicine: How can regulatory science help?

2018 ◽  
Vol 2 (5) ◽  
pp. 295-300
Author(s):  
Joan E. Adamo ◽  
Robert V. Bienvenu ◽  
F. Owen Fields ◽  
Soma Ghosh ◽  
Christina M. Jones ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Precision Medicine ◽  
Working Group ◽  
Regulatory Science ◽  
Translational Science ◽  
Next Generation ◽  
Clinical Validity ◽  
Knowledge Gaps ◽  
Recent Advances ◽  
Generation Sequencing

Building on the recent advances in next-generation sequencing, the integration of genomics, proteomics, metabolomics, and other approaches hold tremendous promise for precision medicine. The approval and adoption of these rapidly advancing technologies and methods presents several regulatory science considerations that need to be addressed. To better understand and address these regulatory science issues, a Clinical and Translational Science Award Working Group convened the Regulatory Science to Advance Precision Medicine Forum. The Forum identified an initial set of regulatory science gaps. The final set of key findings and recommendations provided here address issues related to the lack of standardization of complex tests, preclinical issues, establishing clinical validity and utility, pharmacogenomics considerations, and knowledge gaps.

scholarly journals Diagnosis of Enterococcus faecalis meningitis associated with long-term cerebrospinal fluid rhinorrhoea using metagenomics next-generation sequencing: a case report

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Xiaobo Zhang ◽  
Chao Jiang ◽  
Chaojun Zhou
Keyword(s):  
Cerebrospinal Fluid ◽  
Next Generation Sequencing ◽  
Enterococcus Faecalis ◽  
Bone Defect ◽  
Next Generation ◽  
History Of ◽  
Diagnostic Approaches ◽  
Post Traumatic ◽  
Skull Bone Defect ◽  
Generation Sequencing

Abstract Background Enterococcus faecalis (E. faecalis) meningitis is a rare disease, and most of its occurrences are of post-operative origin. Its rapid diagnosis is critical for effective clinical management. Currently, the diagnosis is focused on cerebrospinal fluid (CSF) culture, but this is quite limited. By comparison, metagenomic next-generation sequencing (mNGS) can overcome the deficiencies of conventional diagnostic approaches. To our knowledge, mNGS analysis of the CSF in the diagnosis of E. faecalis meningitis has been not reported. Case presentation We report the case of E. faecalis meningitis in a 70-year-old female patient without a preceding history of head injury or surgery, but with an occult sphenoid sinus bone defect. Enterococcus faecalis meningitis was diagnosed using mNGS of CSF, and she recovered satisfactorily following treatment with appropriate antibiotics and surgical repair of the skull bone defect. Conclusions Non-post-traumatic or post-surgical E. faecalis meningitis can occur in the presence of occult defects in the cranium, and mNGS technology could be helpful in diagnosis in the absence of a positive CSF culture.

Characterizing the Microbiome of the Contracted Breast Capsule Using Next Generation Sequencing

2020 ◽  
Author(s):  
Jonathan Cook ◽  
Casey J Holmes ◽  
Roger Wixtrom ◽  
Martin I Newman ◽  
Jason N Pozner
Keyword(s):  
Next Generation Sequencing ◽  
Capsular Contracture ◽  
Bacterial Species ◽  
Fungal Species ◽  
Augmentation Mammoplasty ◽  
Next Generation ◽  
Level Of Evidence ◽  
Cutibacterium Acnes ◽  
Microbial Dna ◽  
Generation Sequencing

Abstract Background Recent work suggests that bacterial biofilms play a role in capsular contracture (CC). However, traditional culture techniques provide only a limited understanding of the bacterial communities present within the contracted breast. Next generation sequencing (NGS) represents an evolution of polymerase chain reaction technology that can sequence all DNA present in a given sample. Objectives The aim of this study was to utilize NGS to characterize the bacterial microbiome of the capsule in patients with CC following cosmetic breast augmentation. Methods We evaluated 32 consecutive patients with Baker grade III or IV CC following augmentation mammoplasty. Specimens were obtained from all contracted breasts (n = 53) during capsulectomy. Tissue specimens from contracted capsules as well as intraoperative swabs of the breast capsule and implant surfaces were obtained. Samples were sent to MicroGenDX Laboratories (Lubbock, TX) for NGS. Results Specimens collected from 18 of 32 patients (56%) revealed the presence of microbial DNA. The total number of positive samples was 22 of 53 (42%). Sequencing identified a total of 120 unique bacterial species and 6 unique fungal species. Specimens with microbial DNA yielded a mean [standard deviation] of 8.27 [4.8] microbial species per patient. The most frequently isolated species were Escherichia coli (25% of all isolates), Diaphorobacter nitroreducens (12%), Cutibacterium acnes (12%), Staphylococcus epidermidis (11%), fungal species (7%), and Staphylococcus aureus (6%). Conclusions NGS enables characterization of the bacterial ecosystem surrounding breast implants in unprecedented detail. This is a critical step towards understanding the role this microbiome plays in the development of CC. Level of Evidence: 4

scholarly journals Next-Generation Sequencing in Newborn Screening: A Review of Current State

2021 ◽  
Vol 12 ◽  
Author(s):  
Ziga I. Remec ◽  
Katarina Trebusak Podkrajsek ◽  
Barbka Repic Lampret ◽  
Jernej Kovac ◽  
Urh Groselj ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Newborn Screening ◽  
High Throughput Sequencing ◽  
Successful Implementation ◽  
Next Generation ◽  
Screening Programs ◽  
Sequencing Technologies ◽  
Current State ◽  
Time Required ◽  
Generation Sequencing

Newborn screening was first introduced at the beginning of the 1960s with the successful implementation of the first phenylketonuria screening programs. Early expansion of the included disorders was slow because each additional disorder screened required a separate test. Subsequently, the technological advancements of biochemical methodology enabled the scaling-up of newborn screening, most notably with the implementation of tandem mass spectrometry. In recent years, we have witnessed a remarkable progression of high-throughput sequencing technologies, which has resulted in a continuous decrease of both cost and time required for genetic analysis. This has enabled more widespread use of the massive multiparallel sequencing. Genomic sequencing is now frequently used in clinical applications, and its implementation in newborn screening has been intensively advocated. The expansion of newborn screening has raised many clinical, ethical, legal, psychological, sociological, and technological concerns over time. This review provides an overview of the current state of next-generation sequencing regarding newborn screening including current recommendations and potential challenges for the use of such technologies in newborn screening.

scholarly journals Metagenomics: Retrospect and Prospects in High Throughput Age

2015 ◽  
Vol 2015 ◽  
pp. 1-13 ◽  
Author(s):  
Satish Kumar ◽  
Kishore Kumar Krishnani ◽  
Bharat Bhushan ◽  
Manoj Pandit Brahmane
Keyword(s):  
Community Dynamics ◽  
Full Potential ◽  
Basic Study ◽  
Independent Manner ◽  
Microbial Community Dynamics ◽  
Current State ◽  
Culture Independent ◽  
Almost All ◽  
Insight Into ◽  
Generation Sequencing

In recent years, metagenomics has emerged as a powerful tool for mining of hidden microbial treasure in a culture independent manner. In the last two decades, metagenomics has been applied extensively to exploit concealed potential of microbial communities from almost all sorts of habitats. A brief historic progress made over the period is discussed in terms of origin of metagenomics to its current state and also the discovery of novel biological functions of commercial importance from metagenomes of diverse habitats. The present review also highlights the paradigm shift of metagenomics from basic study of community composition to insight into the microbial community dynamics for harnessing the full potential of uncultured microbes with more emphasis on the implication of breakthrough developments, namely, Next Generation Sequencing, advanced bioinformatics tools, and systems biology.

Next-Generation Sequencing Informing Therapeutic Decisions and Personalized Approaches

2016 ◽  
pp. e442-e448 ◽  
Author(s):  
Raphael Szalat ◽  
Nikhil C. Munshi
Keyword(s):  
Next Generation Sequencing ◽  
High Risk ◽  
Proteasome Inhibitors ◽  
Next Generation ◽  
Current State ◽  
Therapeutic Decisions ◽  
High Risk Disease ◽  
Risk Patients ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Multiple myeloma is a heterogeneous disease featured by different molecular subtypes. In the last decade, new therapeutics including second- and third-generation proteasome inhibitors and immunomodulatory agents, monoclonal antibodies, and other novel targeted agents have completely transformed the outcome of the disease. The task ahead is to develop strategies to identify effective combinations and sequences of agents that can exploit the genetic make-up of myeloma cells to improve efficacy. Moreover, a subgroup of high-risk patients who experience early disease relapse and shorter survival also requires early identification and specific intervention. Next-generation sequencing (NGS) technologies now allow us to accomplish some of these goals. As described here, besides improving our understanding of the disease, it is beginning to influence our clinical decisions and therapeutic choices. In this article, we describe the current state-of-the-art role of NGS in myeloma from identifying high-risk disease, to drug selection, and, ultimately, to guide personalized therapy.

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