The DOI matches its Crossref record; 97 of the 97 references it cites were found in a registry or an index.
Metagenomics for pathogen detection in public health
Open accessAbstract
Traditional pathogen detection methods in public health infectious disease surveillance rely upon the identification of agents that are already known to be associated with a particular clinical syndrome. The emerging field of metagenomics has the potential to revolutionize pathogen detection in public health laboratories by allowing the simultaneous detection of all microorganisms in a clinical sample, without a priori knowledge of their identities, through the use of next-generation DNA sequencing. A single metagenomics analysis has the potential to detect rare and novel pathogens, and to uncover the role of dysbiotic microbiomes in infectious and chronic human disease. Making use of advances in sequencing platforms and bioinformatics tools, recent studies have shown that metagenomics can even determine the whole-genome sequences of pathogens, allowing inferences about antibiotic resistance, virulence, evolution and transmission to be made. We are entering an era in which more novel infectious diseases will be identified through metagenomics-based methods than through traditional laboratory methods. The impetus is now on public health laboratories to integrate metagenomics techniques into their diagnostic arsenals.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Structure, function and diversity of the healthy human microbiome
The Human Microbiome Project Consortium (2012) · Nature · doi:10.1038/nature11234 · Cited by 11,726
Why Most Published Research Findings Are False
Ioannidis, J. P. A. (2005) · PLoS Medicine · doi:10.1371/journal.pmed.0020124 · Cited by 10,505
Global trends in emerging infectious diseases
Jones, K. E., Patel, N. G., Levy, M. A., Storeygard, A., Balk, D., Gittleman, J. L., & Daszak, P. (2008) · Nature · doi:10.1038/nature06536 · Cited by 8,338
A metagenome-wide association study of gut microbiota in type 2 diabetes
Qin, J., Li, Y., Cai, Z., Li, S., Zhu, J., Zhang, F., Liang, S., Zhang, W., Guan, Y., Shen, D., et al. (2012) · Nature · doi:10.1038/nature11450 · Cited by 6,762
Isolation of a Novel Coronavirus from a Man with Pneumonia in Saudi Arabia
Zaki, A. M., van Boheemen, S., Bestebroer, T. M., Osterhaus, A. D. M. E., & Fouchier, R. A. M. (2012) · New England Journal of Medicine · doi:10.1056/nejmoa1211721 · Cited by 5,735
Why Most Published Research Findings Are False
Ioannidis, J. P. A. (2005) · CHANCE · doi:10.1080/09332480.2005.10722754 · Cited by 4,702 · cited 1×
“Research findings are more likely to be true when the prior probability of the finding is high [102]; thus, for unusual metagenomics results, additional lines of evidence are required for confirmation.”
BackgroundEnvironmental genome shotgun sequencing of the sargasso sea
Venter, J. C., Remington, K., Heidelberg, J. F., Halpern, A. L., Rusch, D., Eisen, J. A., Wu, D., Paulsen, I., Nelson, K. E., Nelson, W., et al. (2004) · Science · doi:10.1126/science.1093857 · Cited by 4,376
The human microbiome: at the interface of health and disease
Cho, I., & Blaser, M. J. (2012) · Nature Reviews Genetics · doi:10.1038/nrg3182 · Cited by 3,449
Gut metagenome in European women with normal, impaired and diabetic glucose control
Karlsson, F. H., Tremaroli, V., Nookaew, I., Bergström, G., Behre, C. J., Fagerberg, B., Nielsen, J., & Bäckhed, F. (2013) · Nature · doi:10.1038/nature12198 · Cited by 3,115
A framework for human microbiome research
The Human Microbiome Project Consortium (2012) · Nature · doi:10.1038/nature11209 · Cited by 2,650
Cited by
The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community
Jain, M., Olsen, H. E., Paten, B., & Akeson, M. (2016) · Genome Biology · doi:10.1186/s13059-016-1103-0 · Cited by 1,588
Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software
Sczyrba, A., Hofmann, P., Belmann, P., Koslicki, D., Janssen, S., Dröge, J., Gregor, I., Majda, S., Fiedler, J., Dahms, E., et al. (2017) · Nature Methods · doi:10.1038/nmeth.4458 · Cited by 870
Benchmarking Metagenomics Tools for Taxonomic Classification
Ye, S. H., Siddle, K. J., Park, D. J., & Sabeti, P. C. (2019) · Cell · doi:10.1016/j.cell.2019.07.010 · Cited by 593
Greninger, A. L., Naccache, S. N., Federman, S., Yu, G., Mbala, P., Bres, V., Stryke, D., Bouquet, J., Somasekar, S., Linnen, J. M., et al. (2015) · Genome Medicine · doi:10.1186/s13073-015-0220-9 · Cited by 558
MEGARes: an antimicrobial resistance database for high throughput sequencing
Lakin, S. M., Dean, C., Noyes, N. R., Dettenwanger, A., Ross, A. S., Doster, E., Rovira, P., Abdo, Z., Jones, K. L., Ruiz, J., et al. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkw1009 · Cited by 369
Metadata
- Authors
- Miller, R. R., Montoya, V., Gardy, J. L., Patrick, D. M., & Tang, P.
- Venue
- Genome Medicine
- Published
- 2013
- Volume
- 5
- Issue
- 9
- Pages
- 81
- ISSN
- 1756-994X (ISSN-L)
- OpenAlex
- W2050820276
- Cited by
- 272
- References
- 97
- FWCI
- 4.84
- Type
- journal article
- Language
- en
- Open access
- gold
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
How to cite
Cite CoChat for the checks on this page, and the paper for its own findings.
- This page
- CoChat. (2026). Citation check: Metagenomics for pathogen detection in public health. https://app.cochat.ai/papers/10.1186/gm485
- The paper
- Miller, R. R., Montoya, V., Gardy, J. L., Patrick, D. M., & Tang, P. (2013). Metagenomics for pathogen detection in public health. Genome Medicine. https://doi.org/10.1186/gm485
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
