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Hot Topics of the Day are picked by experts to capture the latest information and publications on public health genomics and precision health for various diseases and health topics. Sources include published scientific literature, reviews, blogs and popular press articles.

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63 hot topic(s) found with the query "Metagenomics"

Metagenomic sequencing of post-mortem tissue samples for the identification of pathogens associated with neonatal deaths.
Vicky L Baillie et al. Nat Commun 2023 9 (1) 5373 (Posted: Sep 05, 2023 9AM)

From the abstract: " In this study, metagenomic next generation sequencing was used to explore for putative pathogens associated with neonatal deaths in post-mortem blood and lung tissue samples, in Soweto, South Africa. Here we show that the metagenomic sequencing results corroborate the findings using conventional methods of culture and nucleic acid amplifications tests on post-mortem samples in detecting the pathogens attributed in the causal pathway of death in 90% (18/20) of the decedents."

From Mendel to multi-omics: shifting paradigms
TB Mersha, EJHG, July 20, 2023 (Posted: Jul 20, 2023 7AM)

Multi-omics analysis is an emerging approach that aims to better understand health and disease through the convergence of different omics studies (genomics, transcriptomics, proteomics, metabolomics, metagenomics, phenomics, exposomics). Although technical limitations related to the analysis of high-dimensional multi-omics datasets and use of fairly small samples have hindered our ability to conduct multi-omic research, emerging technology and computational tools have facilitated impactful multi-omic research.

Gut microbial metabolism of 5-ASA diminishes its clinical efficacy in inflammatory bowel disease.
Raaj S Mehta et al. Nature medicine 2023 2 (Posted: Feb 24, 2023 7AM)

We developed a multi-omics workflow combining gut microbiome metagenomics, metatranscriptomics and metabolomics from the longitudinal IBDMDB cohort of 132 controls and patients with IBD. This associated 12 previously uncharacterized microbial acetyltransferases with 5-ASA inactivation, belonging to two protein superfamilies: thiolases and acyl-CoA N-acyltransferases. A cross-sectional analysis within the discovery cohort and subsequent prospective validation within the independent SPARC IBD cohort (n?=?208) found three of these microbial thiolases and one acyl-CoA N-acyltransferase to be epidemiologically associated with an increased risk of treatment failure among 5-ASA users.

Combining pathogen and host metagenomics for a better sepsis diagnostic.
Gant Vanya et al. Nature microbiology 2022 10 (11) 1713-1714 (Posted: Oct 29, 2022 11AM)

Sepsis is defined in the clinic as an assemblage of various failing physiology and laboratory markers of organ function triggered by infection. Efforts have been made to provide tighter definitions and criteria for sepsis to achieve better and more focused clinical care, research and epidemiology. A recent study shows that combining simultaneous host and pathogen metagenomic profiles in a cohort of hospitalized and critically ill patients allows for more accurate diagnosis of sepsis.

Integrated host-microbe plasma metagenomics for sepsis diagnosis in a prospective cohort of critically ill adults.
Kalantar Katrina L et al. Nature microbiology 2022 10 (Posted: Oct 22, 2022 11AM)

We combined host and microbial features to develop an integrated sepsis diagnostic model that identified 99% of microbiologically confirmed sepsis cases, and predicted sepsis in 74% of suspected and 89% of indeterminate sepsis cases. We suggest that integrating host transcriptional profiling and broad-range metagenomic pathogen detection from nucleic acid is a promising tool for sepsis diagnosis.

The Current Status of Next-Generation Sequencing for Diagnosis of Central Nervous System Infections
MR Wilson et al, JAMA Neurology, August 22, 2022 (Posted: Aug 22, 2022 4PM)

The prime directive in diagnosing neuroinfectious disease is to answer 3 deceptively simple questions: (1) Is the patient infected? (2) If so, with what? (3) How do we treat the infection? Our ability to answer the first 2 questions has been substantially improved by the emergence of multiplex approaches to diagnosis of central nervous system (CNS) infections, as exemplified by metagenomic next-generation sequencing (mNGS).

Phylogenomic characterization and signs of microevolution in the 2022 multi-country outbreak of monkeypox virus
J Isidro et al, Nature Medicine, June 25, 2022 (Posted: Jun 25, 2022 11AM)

Here, shotgun metagenomics allowed the rapid reconstruction and phylogenomic characterization of the first MPXV outbreak genome sequences, showing that this MPXV belongs to clade 3 and that the outbreak most likely has a single origin. Although 2022 MPXV (lineage B.1) clustered with 2018-2019 cases linked to an endemic country, it segregates in a divergent phylogenetic branch, likely reflecting continuous accelerated evolution.

The Role of Metagenomics and Next-Generation Sequencing in Infectious Disease Diagnosis.
Miller Steve et al. Clinical chemistry 2021 68(1) 115-124 (Posted: Jan 04, 2022 10AM)

Most studies demonstrate that mNGS has sensitivity similar to specific PCR assays and will identify more potential pathogens than conventional methods. While many of these additional organism detections correlate with the expected pathogen spectrum based on patient presentations, there are relatively few formal studies demonstrating whether these are true-positive infections and benefits to clinical outcomes. Reduced specificity due to contamination and clinically nonsignificant organism detections remains a major concern, emphasizing the importance of careful interpretation of the organism pathogenicity and potential association with the clinical syndrome.

Evaluating the potential for respiratory metagenomics to improve treatment of secondary infection and detection of nosocomial transmission on expanded COVID-19 intensive care units
T Charalampous et al, Genome Medicine, November 17, 2021 (Posted: Nov 17, 2021 10AM)

Clinical metagenomics (CMg) has the potential to be translated from a research tool into routine service to improve antimicrobial treatment and infection control decisions. The SARS-CoV-2 pandemic provides added impetus to realise these benefits, given the increased risk of secondary infection and nosocomial transmission of multi-drug-resistant (MDR) pathogens linked with the expansion of critical care capacity.

Discovering disease-causing pathogens in resource-scarce Southeast Asia using a global metagenomic pathogen monitoring system
JA Bohl et al, MEDRXIV, September 28, 2021 (Posted: Sep 29, 2021 5AM)

Understanding the regional pathogen landscape and surveillance of emerging pathogens is key to mitigating epidemics. Challenges lie in resource-scarce settings, where outbreaks are likely to emerge, but where laboratory diagnostics and bioinformatics capacity are limited. Using unbiased metagenomic next generation sequencing (mNGS), we identified a variety of vector-borne, zoonotic and emerging pathogens responsible for undifferentiated fevers in a peri-urban population in Cambodia.

Detection of Neoplasms by Metagenomic Next-Generation Sequencing of Cerebrospinal Fluid
W Gu et al, JAMA Network Open, September 13, 2021 (Posted: Sep 14, 2021 6AM)

Can metagenomic next-generation sequencing (mNGS) of cerebrospinal fluid (CSF), a test designed to diagnose neurological infections, also detect genetic signatures of cancer in patients with presentations that are suggestive of neuroinflammatory disease? In this case-control study of 130 patients, many of whom with negative CSF cytologic testing and/or flow cytometry results, CSF mNGS detected genetic evidence for a malignant neoplasm, with a sensitivity of 75% and specificity of 100%.

The Disease Detective: Joe DeRisi invented a way to find pathogens that scientists didn’t even know to look for. Can it help prevent the next pandemic?
J Kahn, June 3, NY Times, June 5, 2021 (Posted: Jun 06, 2021 7AM)

The white box, when connected to an elaborate analysis system DeRisi had designed, allowed researchers from around the world to piece together all the different DNA or RNA recovered from just about any sample — throat swabs, blood draws or other material — and scan it for unidentified pathogens.

Targeted Hybridization Capture of SARS-CoV-2 and Metagenomics Enables Genetic Variant Discovery and Nasal Microbiome Insights
DN Szakal et al, MEDRXIV, March 20, 2021 (Posted: Mar 20, 2021 0PM)

Translating the microbiome in health and disease
Genome Medicine special issue, October 2020 (Posted: Oct 23, 2020 7AM)

This issue captures insights into the human microbiome in health and disease including standards for microbiome analyses in basic and clinical research, microbiome analysis technologies, metagenomics and integrative multi-omics, antibiotics and the microbiome, microbial biochemistry and diet, translational interventions, and host-microbiome interactions.

Microbiome and health implications for ethnic minorities after enforced lifestyle changes
DM Keohane et al, Nature Medicine, July 6, 2020 (Posted: Jul 06, 2020 11AM)

Comparative metagenomics of gut microbiomes shows that Irish Travellers retain a microbiota similar to that of non-industrialized societies. Their microbiota is associated with non-dietary factors and is proportionately linked with risk of microbiome-related metabolic disease.

Real-time Metagenomic Analysis of Undiagnosed Fever Cases Unveils a Yellow Fever Outbreak in Edo State, Nigeria
Scientific Reports, February 2020 (Posted: Mar 04, 2020 8AM)

Shotgun metagenomics: A promising new method toward diagnosing infections
S Rosen, Mayo clinic Blog, September 2019 (Posted: Sep 10, 2019 9AM)

Shotgun metagenomic sequencing is a new way to detect infectious organisms. Currently, this technology is undergoing validation for clinical testing. Traditional microbiology has not always been able to do this because certain microorganisms cannot be grown in culture.

Hybrid metagenomic assembly enables high-resolution analysis of resistance determinants and mobile elements in human microbiomes
D Bertrand et al, Nature Biotechnology, July 29, 2019 (Posted: Jul 29, 2019 1PM)

Metagenomic identification of severe pneumonia pathogens with rapid Nanopore sequencing in mechanically-ventilated patients.
L Yang et al, MedXRIV preprints, July 24, 2019 (Posted: Jul 24, 2019 8AM)

Metagenomic sequencing of respiratory microbial communities for etiologic pathogen identification in pneumonia may help overcome the limitations of current culture-based methods. The study examined the feasibility and clinical validity of rapid-turnaround metagenomics with Nanopore sequencing of respiratory samples for severe pneumonia diagnosis.

Clinical Metagenomic Sequencing for Diagnosis of Meningitis and Encephalitis.
Wilson Michael R et al. The New England journal of medicine 2019 Jun (24) 2327-2340 (Posted: Jun 13, 2019 0PM)

Clinical metagenomics
CY Chiu et al, Nature Rev Genetics, March 27, 2019 (Posted: Mar 27, 2019 2PM)

Using targeted and metagenomic sequencing to identify and characterize pathogens in unknown respiratory disease outbreaks
CDC, AMD projects Brand (Posted: Oct 22, 2018 5PM)

DNA Tests Could Help Docs Detect Infectious Diseases Faster
M Molteni, Wired, October 22, 2018 (Posted: Oct 22, 2018 5PM)

A Simpler Way to Get to the Bottom of Mysterious Illnesses in Poor Countries
E Yong, the Atlantic, October 16, 2018 (Posted: Oct 18, 2018 8AM)

Machine learning spots treasure trove of elusive viruses- Artificial intelligence could speed up metagenomic studies that look for species unknown to science.
A Maxmen, Nature, Mar 2018 (Posted: Apr 09, 2018 1PM)

Whole metagenome sequencing reveals links between mosquito microbiota and insecticide resistance in malaria vectors.
Dada Nsa et al. Scientific reports 2018 Feb (1) 2084 (Posted: Feb 06, 2018 3PM)

Virus discovery by metagenomics: the (im)possibilities
Frontiers Research Topic, Oct 2017 (Posted: Oct 28, 2017 2PM)

Shotgun metagenomics, from sampling to analysis.
Quince Christopher et al. Nature biotechnology 2017 Sep (9) 833-844 (Posted: Sep 13, 2017 9AM)

Presence of Human Hepegivirus-1 in a Cohort of People Who Inject Drugs.
Kandathil Abraham J et al. Annals of internal medicine 2017 Jun (Posted: Jun 15, 2017 3PM)

Source code: Putting metagenomics to the test in the clinic.
Arnold Carrie et al. Nature medicine 2017 Jun (6) 645-648 (Posted: Jun 07, 2017 8AM)

Environmental Viral Metagenomics Analyses in Aquaculture: Applications in Epidemiology and Disease Control.
Munang'andu Hetron M et al. Frontiers in microbiology 2016 1986 (Posted: Feb 10, 2017 3PM)

Consensus statement: Virus taxonomy in the age of metagenomics.
Simmonds Peter et al. Nature reviews. Microbiology 2017 Jan (Posted: Feb 10, 2017 3PM)

Validation of Metagenomic Next-Generation Sequencing Tests for Universal Pathogen Detection.
Schlaberg Robert et al. Archives of pathology & laboratory medicine 2017 Feb (Posted: Feb 10, 2017 3PM)

Metagenomics of two severe foodborne outbreaks provides diagnostic signatures and signs of co-infection not attainable by traditional methods.
Huang Andrew D et al. Applied and environmental microbiology 2016 Nov (Posted: Dec 07, 2016 9AM)

Translational metagenomics and the human resistome: confronting the menace of the new millennium.
Willmann Matthias et al. Journal of molecular medicine (Berlin, Germany) 2016 Oct (Posted: Nov 02, 2016 6AM)

Genomic and functional techniques to mine the microbiome for novel antimicrobials and antimicrobial resistance genes.
Adu-Oppong Boahemaa et al. Annals of the New York Academy of Sciences 2016 Oct (Posted: Nov 02, 2016 6AM)

Viral Metagenomics on Blood-Feeding Arthropods as a Tool for Human Disease Surveillance.
Brinkmann Annika et al. International journal of molecular sciences 2016 Oct (10) (Posted: Nov 02, 2016 6AM)

Finding the Needle in the Haystack: Using Metagenomics to Diagnose Infections and Control Disease Outbreaks
Brand (Posted: Nov 02, 2016 6AM)

Functional Metagenomics as a Tool for Identification of New Antibiotic Resistance Genes from Natural Environments.
Dos Santos Débora Farage Knupp et al. Microbial ecology 2016 Oct (Posted: Oct 07, 2016 8AM)

Metagenomic applications in environmental monitoring and bioremediation.
Techtmann Stephen M et al. Journal of industrial microbiology & biotechnology 2016 Aug (Posted: Aug 26, 2016 8AM)

Toward Accurate and Quantitative Comparative Metagenomics
S Nayfash et al, Cell, August 2016 (Posted: Aug 26, 2016 8AM)

Recent progress in genetics, epigenetics and metagenomics unveils the pathophysiology of human obesity.
Pigeyre Marie et al. Clinical science (London, England : 1979) 2016 Jun (12) 943-86 (Posted: Jul 25, 2016 9PM)

The Challenge and Potential of Metagenomics in the Clinic.
Mulcahy-O'Grady Heidi et al. Frontiers in immunology 2016 29 (Posted: Feb 17, 2016 5PM)

The Road to Metagenomics: From Microbiology to DNA Sequencing Technologies and Bioinformatics.
Escobar-Zepeda Alejandra et al. Frontiers in genetics 2015 348 (Posted: Feb 15, 2016 3PM)

Using whole genome sequencing and metagenomics to identify and track tickborne pathogens
Brand (Posted: Feb 08, 2016 2PM)

Metagenomic cross-talk: the regulatory interplay between immunogenomics and the microbiome.
Levy Maayan et al. Genome medicine (1) 120 (Posted: Nov 24, 2015 9AM)

Metagenomics: A New Way to Illustrate the Crosstalk between Infectious Diseases and Host Microbiome.
Zhang Yinfeng et al. International journal of molecular sciences 2015 (11) 26263-79 (Posted: Nov 07, 2015 0PM)

Metagenomics: tools and insights for analyzing next-generation sequencing data derived from biodiversity studies.
Oulas Anastasis et al. Bioinform Biol Insights 2015 75-88 (Posted: Aug 19, 2015 0PM)

Meta-genomic analysis of toilet waste from long distance flights; a step towards global surveillance of infectious diseases and antimicrobial resistance.
Nordahl Petersen Thomas et al. Sci Rep 2015 11444 (Posted: Aug 19, 2015 0PM)

Challenges and opportunities of airborne metagenomics.
Behzad Hayedeh et al. Genome Biol Evol 2015 May (5) 1216-26 (Posted: Aug 19, 2015 0PM)

Metagenomics meets time series analysis: unraveling microbial community dynamics.
Faust Karoline et al. Curr. Opin. Microbiol. 2015 Jun 56-66 (Posted: Aug 19, 2015 0PM)

Metagenomics of extreme environments.
Cowan D A et al. Curr. Opin. Microbiol. 2015 Jun 97-102 (Posted: Aug 19, 2015 0PM)

Metagenomics: A new horizon in cancer research.
Banerjee Joyita et al. Meta Gene 2015 Sep 84-9 (Posted: Aug 19, 2015 0PM)

Combining metagenomics, metatranscriptomics and viromics to explore novel microbial interactions: towards a systems-level understanding of human microbiome.
Bikel Shirley et al. Comput Struct Biotechnol J 2015 390-401 (Posted: Aug 19, 2015 0PM)

From cultured to uncultured genome sequences: metagenomics and modeling microbial ecosystems.
Garza Daniel R et al. Cell. Mol. Life Sci. 2015 Aug 9. (Posted: Aug 19, 2015 0PM)

Next-generation sequencing in clinical virology: Discovery of new viruses.
Datta Sibnarayan et al. World J Virol 2015 Aug 12. (3) 265-76 (Posted: Aug 19, 2015 0PM)

Proteomics as the final step in the functional metagenomics study of antimicrobial resistance.
Fouhy Fiona et al. Front Microbiol 2015 172 (Posted: Mar 30, 2015 5PM)

Beyond research: a primer for considerations on using viral metagenomics in the field and clinic
RJ Hall et al. Frontiers in Microbiology, 2015 (Posted: Mar 06, 2015 2PM)

The Newest "Omics"-Metagenomics and Metabolomics-Enter the Battle against the Neglected Tropical Diseases.
Preidis Geoffrey A et al. PLoS Negl Trop Dis 2015 Feb (2) e0003382 (Posted: Mar 06, 2015 2PM)

'Metagenomics 2.0'.
McMahon Katherine et al. Environ Microbiol Rep 2015 Feb (1) 38-9 (Posted: Mar 06, 2015 2PM)

Metagenomics: Urban microbiome.
Bahcall Orli G et al. Nat. Rev. Genet. 2015 Mar 3. (Posted: Mar 06, 2015 2PM)

Application of metagenomics in understanding oral health and disease.
Xu Ping et al. Virulence 2014 Apr 1. (3) 424-32 (Posted: Mar 06, 2015 0PM)

Insights into ancient leprosy and tuberculosis using metagenomics.
Donoghue Helen D et al. Trends in microbiology 2013 Sep (9) 448-50 (Posted: Feb 12, 2015 8AM)


Disclaimer: Articles listed in Hot Topics of the Day are selected by Public Health Genomics Branch to provide current awareness of the scientific literature and news. Inclusion in the update does not necessarily represent the views of the Centers for Disease Control and Prevention nor does it imply endorsement of the article's methods or findings. CDC and DHHS assume no responsibility for the factual accuracy of the items presented. The selection, omission, or content of items does not imply any endorsement or other position taken by CDC or DHHS. Opinion, findings and conclusions expressed by the original authors of items included in the Clips, or persons quoted therein, are strictly their own and are in no way meant to represent the opinion or views of CDC or DHHS. References to publications, news sources, and non-CDC Websites are provided solely for informational purposes and do not imply endorsement by CDC or DHHS.
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