The DOI matches its Crossref record; 39 of the 39 references it cites were found in a registry or an index.
Metagenomic Assembly Reveals Hosts of Antibiotic Resistance Genes and the Shared Resistome in Pig, Chicken, and Human Feces
Abstract
The risk associated with antibiotic resistance disseminating from animal and human feces is an urgent public issue. In the present study, we sought to establish a pipeline for annotating antibiotic resistance genes (ARGs) based on metagenomic assembly to investigate ARGs and their co-occurrence with associated genetic elements. Genetic elements found on the assembled genomic fragments include mobile genetic elements (MGEs) and metal resistance genes (MRGs). We then explored the hosts of these resistance genes and the shared resistome of pig, chicken and human fecal samples. High levels of tetracycline, multidrug, erythromycin, and aminoglycoside resistance genes were discovered in these fecal samples. In particular, significantly high level of ARGs (7762 ×/Gb) was detected in adult chicken feces, indicating higher ARG contamination level than other fecal samples. Many ARGs arrangements (e.g., macA-macB and tetA-tetR) were discovered shared by chicken, pig and human feces. In addition, MGEs such as the aadA5-dfrA17-carrying class 1 integron were identified on an assembled scaffold of chicken feces, and are carried by human pathogens. Differential coverage binning analysis revealed significant ARG enrichment in adult chicken feces. A draft genome, annotated as multidrug resistant Escherichia coli, was retrieved from chicken feces metagenomes and was determined to carry diverse ARGs (multidrug, acriflavine, and macrolide). The present study demonstrates the determination of ARG hosts and the shared resistome from metagenomic data sets and successfully establishes the relationship between ARGs, hosts, and environments. This ARG annotation pipeline based on metagenomic assembly will help to bridge the knowledge gaps regarding ARG-associated genes and ARG hosts with metagenomic data sets. Moreover, this pipeline will facilitate the evaluation of environmental risks in the genetic context of ARGs.
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
From genomics to chemical genomics: new developments in KEGG
Kanehisa, M. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkj102 · Cited by 3,120
Antibiotic resistance is ancient
D’Costa, V. M., King, C. E., Kalan, L., Morar, M., Sung, W. W. L., Schwarz, C., Froese, D., Zazula, G., Calmels, F., Debruyne, R., et al. (2011) · Nature · doi:10.1038/nature10388 · Cited by 2,720
Diverse and abundant antibiotic resistance genes in Chinese swine farms
Zhu, Y.-G., Johnson, T. A., Su, J.-Q., Qiao, M., Guo, G.-X., Stedtfeld, R. D., Hashsham, S. A., & Tiedje, J. M. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1222743110 · Cited by 2,440
Self-citationCo-selection of antibiotic and metal resistance
Baker-Austin, C., Wright, M. S., Stepanauskas, R., & McArthur, J. V. (2006) · Trends in Microbiology · doi:10.1016/j.tim.2006.02.006 · Cited by 1,883
Ab initio gene identification in metagenomic sequences
Zhu, W., Lomsadze, A., & Borodovsky, M. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq275 · Cited by 1,819
The shared antibiotic resistome of soil bacteria and human pathogens
Forsberg, K. J., Reyes, A., Wang, B., Selleck, E. M., Sommer, M. O. A., & Dantas, G. (2012) · Science · doi:10.1126/science.1220761 · Cited by 1,650
Integrative analysis of environmental sequences using MEGAN4
Huson, D. H., Mitra, S., Ruscheweyh, H.-J., Weber, N., & Schuster, S. C. (2011) · Genome Research · doi:10.1101/gr.120618.111 · Cited by 1,541
Albertsen, M., Hugenholtz, P., Skarshewski, A., Nielsen, K. L., Tyson, G. W., & Nielsen, P. H. (2013) · Nature Biotechnology · doi:10.1038/nbt.2579 · Cited by 1,251
Li, B., Yang, Y., Ma, L., Ju, F., Guo, F., Tiedje, J. M., & Zhang, T. (2015) · The ISME Journal · doi:10.1038/ismej.2015.59 · Cited by 1,238
Self-citationSeiler, C., & Berendonk, T. U. (2012) · Frontiers in Microbiology · doi:10.3389/fmicb.2012.00399 · Cited by 1,018
Metagenome-wide analysis of antibiotic resistance genes in a large cohort of human gut microbiota
Hu, Y., Yang, X., Qin, J., Lu, N., Cheng, G., Wu, N., Pan, Y., Li, J., Zhu, L., Wang, X., et al. (2013) · Nature Communications · doi:10.1038/ncomms3151 · Cited by 781
Self-citationGenomic insights to SAR86, an abundant and uncultivated marine bacterial lineage
Dupont, C. L., Rusch, D. B., Yooseph, S., Lombardo, M.-J., Alexander Richter, R., Valas, R., Novotny, M., Yee-Greenbaum, J., Selengut, J. D., Haft, D. H., et al. (2012) · The ISME Journal · doi:10.1038/ismej.2011.189 · Cited by 519
Antibiotics in animal feed and their role in resistance development
Wegener, H. C. (2003) · Current Opinion in Microbiology · doi:10.1016/j.mib.2003.09.009 · Cited by 517
Fate of antibiotic resistance genes in sewage treatment plant revealed by metagenomic approach
Yang, Y., Li, B., Zou, S., Fang, H. H. P., & Zhang, T. (2014) · Water Research · doi:10.1016/j.watres.2014.05.019 · Cited by 512
Self-citationSmith, D. L., Harris, A. D., Johnson, J. A., Silbergeld, E. K., & Morris, J. G. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.082188899 · Cited by 463
Marti, R., Scott, A., Tien, Y.-C., Murray, R., Sabourin, L., Zhang, Y., & Topp, E. (2013) · Applied and Environmental Microbiology · doi:10.1128/aem.01682-13 · Cited by 450
Chen, B., Yang, Y., Liang, X., Yu, K., Zhang, T., & Li, X. (2013) · Environmental Science & Technology · doi:10.1021/es403818e · Cited by 415
Self-citationZhang, T., Zhang, X.-X., & Ye, L. (2011) · PLoS ONE · doi:10.1371/journal.pone.0026041 · Cited by 400
Self-citationYang, Y., Li, B., Ju, F., & Zhang, T. (2013) · Environmental Science & Technology · doi:10.1021/es4017365 · Cited by 360
Self-citationWu, N., Qiao, M., Zhang, B., Cheng, W.-D., & Zhu, Y.-G. (2010) · Environmental Science & Technology · doi:10.1021/es1007802 · Cited by 355
Leverstein‐van Hall, M. A., M. Blok, H. E., T. Donders, A. R., Paauw, A., Fluit, A. C., & Verhoef, J. (2003) · The Journal of Infectious Diseases · doi:10.1086/345880 · Cited by 281
Zhang, X., & Zhang, T. (2011) · Environmental Science & Technology · doi:10.1021/es103672x · Cited by 272
Self-citationDistribution of antibiotic resistance genes in glacier environments
Segawa, T., Takeuchi, N., Rivera, A., Yamada, A., Yoshimura, Y., Barcaza, G., Shinbori, K., Motoyama, H., Kohshima, S., & Ushida, K. (2013) · Environmental Microbiology Reports · doi:10.1111/1758-2229.12011 · Cited by 220
Swick, M. C., Morgan-Linnell, S. K., Carlson, K. M., & Zechiedrich, L. (2011) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.00996-10 · Cited by 219
Totsika, M., Beatson, S. A., Sarkar, S., Phan, M.-D., Petty, N. K., Bachmann, N., Szubert, M., Sidjabat, H. E., Paterson, D. L., Upton, M., et al. (2011) · PLoS ONE · doi:10.1371/journal.pone.0026578 · Cited by 218
Ishii, S., Suzuki, S., Norden-Krichmar, T. M., Tenney, A., Chain, P. S. G., Scholz, M. B., Nealson, K. H., & Bretschger, O. (2013) · Nature Communications · doi:10.1038/ncomms2615 · Cited by 204
Detection of a Streptomycin/Spectinomycin Adenylyltransferase Gene ( aadA ) in Enterococcus faecalis
Clark, N. C., Olsvik, Ø., Swenson, J. M., Spiegel, C. A., & Tenover, F. C. (1999) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.43.1.157 · Cited by 202
Christgen, B., Yang, Y., Ahammad, S. Z., Li, B., Rodriquez, D. C., Zhang, T., & Graham, D. W. (2015) · Environmental Science & Technology · doi:10.1021/es505521w · Cited by 189
Self-citationChagas, T. P. G., Seki, L. M., Cury, J. C., Oliveira, J. A. L., Dávila, A. M. R., Silva, D. M., & Asensi, M. D. (2011) · Journal of Applied Microbiology · doi:10.1111/j.1365-2672.2011.05072.x · Cited by 177
Sunde, M., & Norström, M. (2006) · Journal of Antimicrobial Chemotherapy · doi:10.1093/jac/dkl294 · Cited by 153
Community-wide plasmid gene mobilization and selection
Sentchilo, V., Mayer, A. P., Guy, L., Miyazaki, R., Green, S., Barry, K., Malfatti, S., Goessmann, A., Robinson‐Rechavi, M., & van der Meer, J. R. (2013) · The ISME Journal · doi:10.1038/ismej.2013.13 · Cited by 132
Chao, Y., Ma, L., Yang, Y. J., Ju, F., Zhang, X., Wu, W., & Zhang, T. (2013) · Scientific Reports · doi:10.1038/srep03550 · Cited by 114
Self-citationYang, J., Wang, C., Shu, C., Liu, L., Geng, J., Hu, S., & Feng, J. (2013) · Microbial Ecology · doi:10.1007/s00248-013-0187-2 · Cited by 104
Ma, L., Li, B. J., & Zhang, T. (2014) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-014-5511-3 · Cited by 90
Self-citationYu, H. S. (2004) · Journal of Antimicrobial Chemotherapy · doi:10.1093/jac/dkh097 · Cited by 65
Pasterán, F. G., Faccone, D. F., Petroni, A., Rapoport, M., Galas, M., Vázquez, M., & Procopio, A. (2004) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.49.1.474-475.2005 · Cited by 63
Mao, Y., Xia, Y., Wang, Z., & Zhang, T. (2014) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-014-5756-x · Cited by 52
Self-citationIdentification of antimicrobial resistant bacteria in rivers: Insights into the cultivation bias
García–Armisen, T., Anzil, A., Cornélis, P., Chevreuil, M., & Servais, P. (2013) · Water Research · doi:10.1016/j.watres.2013.05.036 · Cited by 37
Chakraborty, R., Kumar, A., Bhowal, S. S., Mandal, A. K., Tiwary, B. K., & Mukherjee, S. (2013) · PLoS ONE · doi:10.1371/journal.pone.0071753 · Cited by 17
Cited by
Co-occurrence of antibiotic and metal resistance genes revealed in complete genome collection
Li, L.-G., Xia, Y., & Zhang, T. (2017) · The ISME Journal · doi:10.1038/ismej.2016.155 · Cited by 528
Self-citationDistribution of antibiotic resistance genes in the environment
Zhuang, M., Achmon, Y., Cao, Y., Liang, X., Chen, L., Wang, H., Siame, B. A., & Leung, K. Y. (2021) · Environmental Pollution · doi:10.1016/j.envpol.2021.117402 · Cited by 422
Zhao, R., Feng, J., Liu, J., Fu, W., Li, X., & Li, B. (2019) · Water Research · doi:10.1016/j.watres.2018.12.034 · Cited by 383
Self-citationXie, J., Jin, L., Luo, X., Zhao, Z., & Li, X. (2018) · Environmental Science & Technology Letters · doi:10.1021/acs.estlett.7b00561 · Cited by 161
Ren, C.-Y., Wu, E.-L., Hartmann, E. M., & Zhao, H.-P. (2021) · Environmental Science & Technology · doi:10.1021/acs.est.1c04641 · Cited by 73
Metadata
- Authors
- Ma, L., Xia, Y., Li, B., Yang, Y., Li, L.-G., Tiedje, J. M., & Zhang, T.
- Venue
- Environmental Science & Technology
- Publisher
- American Chemical Society (ACS)
- Published
- 2015-12-22
- Volume
- 50
- Issue
- 1
- Pages
- 420-427
- ISSN
- 0013-936X (ISSN-L)
- 1520-5851
- OpenAlex
- W2227972161
- Cited by
- 423
- References
- 39
- FWCI
- 5.76
- Type
- journal article
- Language
- en
- Open access
- closed
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
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.
