Species-resolved profiling of antibiotic resistance genes in complex metagenomes through long-read overlapping with Argo
Author
Abstract
Suggested Citation
DOI: 10.1038/s41467-025-57088-y
Download full text from publisher
References listed on IDEAS
- Rene S. Hendriksen & Patrick Munk & Patrick Njage & Bram Bunnik & Luke McNally & Oksana Lukjancenko & Timo Röder & David Nieuwenhuijse & Susanne Karlsmose Pedersen & Jette Kjeldgaard & Rolf S. Kaas & , 2019. "Global monitoring of antimicrobial resistance based on metagenomics analyses of urban sewage," Nature Communications, Nature, vol. 10(1), pages 1-12, December.
- Liang Chen & Na Zhao & Jiabao Cao & Xiaolin Liu & Jiayue Xu & Yue Ma & Ying Yu & Xuan Zhang & Wenhui Zhang & Xiangyu Guan & Xiaotong Yu & Zhipeng Liu & Yanqun Fan & Yang Wang & Fan Liang & Depeng Wang, 2022. "Short- and long-read metagenomics expand individualized structural variations in gut microbiomes," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
- Cong Wang & Qing-Yi Yu & Niu-Niu Ji & Yong Zheng & John W. Taylor & Liang-Dong Guo & Cheng Gao, 2023. "Bacterial genome size and gene functional diversity negatively correlate with taxonomic diversity along a pH gradient," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
- Jean-Sebastien Gounot & Minghao Chia & Denis Bertrand & Woei-Yuh Saw & Aarthi Ravikrishnan & Adrian Low & Yichen Ding & Amanda Hui Qi Ng & Linda Wei Lin Tan & Yik-Ying Teo & Henning Seedorf & Niranjan, 2022. "Genome-centric analysis of short and long read metagenomes reveals uncharacterized microbiome diversity in Southeast Asians," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
- Alexander T. Dilthey & Chirag Jain & Sergey Koren & Adam M. Phillippy, 2019. "Strain-level metagenomic assignment and compositional estimation for long reads with MetaMaps," Nature Communications, Nature, vol. 10(1), pages 1-12, December.
- Kihyun Lee & Sebastien Raguideau & Kimmo Sirén & Francesco Asnicar & Fabio Cumbo & Falk Hildebrand & Nicola Segata & Chang-Jun Cha & Christopher Quince, 2023. "Population-level impacts of antibiotic usage on the human gut microbiome," Nature Communications, Nature, vol. 14(1), pages 1-19, December.
- An-Ni Zhang & Jeffry M. Gaston & Chengzhen L. Dai & Shijie Zhao & Mathilde Poyet & Mathieu Groussin & Xiaole Yin & Li-Guan Li & Mark C. M. Loosdrecht & Edward Topp & Michael R. Gillings & William P. H, 2021. "An omics-based framework for assessing the health risk of antimicrobial resistance genes," Nature Communications, Nature, vol. 12(1), pages 1-11, December.
Most related items
These are the items that most often cite the same works as this one and are cited by the same works as this one.- Yi-Fei Wang & Yan-Jie Liu & Yan-Mei Fu & Jia-Yang Xu & Tian-Lun Zhang & Hui-Ling Cui & Min Qiao & Matthias C. Rillig & Yong-Guan Zhu & Dong Zhu, 2024. "Microplastic diversity increases the abundance of antibiotic resistance genes in soil," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
- Zhenyan Zhang & Qi Zhang & Tingzhang Wang & Nuohan Xu & Tao Lu & Wenjie Hong & Josep Penuelas & Michael Gillings & Meixia Wang & Wenwen Gao & Haifeng Qian, 2022. "Assessment of global health risk of antibiotic resistance genes," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
- Achal Dhariwal & Polona Rajar & Gabriela Salvadori & Heidi Aarø Åmdal & Dag Berild & Ola Didrik Saugstad & Drude Fugelseth & Gorm Greisen & Ulf Dahle & Kirsti Haaland & Fernanda Cristina Petersen, 2024. "Prolonged hospitalization signature and early antibiotic effects on the nasopharyngeal resistome in preterm infants," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
- Ernest D. Osburn & Steven G. McBride & Mohammad Bahram & Michael S. Strickland, 2024. "Global patterns in the growth potential of soil bacterial communities," Nature Communications, Nature, vol. 15(1), pages 1-9, December.
- Patrick Munk & Christian Brinch & Frederik Duus Møller & Thomas N. Petersen & Rene S. Hendriksen & Anne Mette Seyfarth & Jette S. Kjeldgaard & Christina Aaby Svendsen & Bram Bunnik & Fanny Berglund & , 2022. "Genomic analysis of sewage from 101 countries reveals global landscape of antimicrobial resistance," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
- Andrea Butcher & Jose A. Cañada & Salla Sariola, 2021. "How to make noncoherent problems more productive: Towards an AMR management plan for low resource livestock sectors," Palgrave Communications, Palgrave Macmillan, vol. 8(1), pages 1-10, December.
- Qi Dang & Wei Zhang & Jiqing Liu & Liting Wang & Deli Wu & Dejin Wang & Zhendong Lei & Liang Tang, 2023. "Bias-free driven ion assisted photoelectrochemical system for sustainable wastewater treatment," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
- Kihyun Lee & Sebastien Raguideau & Kimmo Sirén & Francesco Asnicar & Fabio Cumbo & Falk Hildebrand & Nicola Segata & Chang-Jun Cha & Christopher Quince, 2023. "Population-level impacts of antibiotic usage on the human gut microbiome," Nature Communications, Nature, vol. 14(1), pages 1-19, December.
- Aguiar, Raphael & Keil, Roger & Wiktorowicz, Mary, 2024. "The urban political ecology of antimicrobial resistance: A critical lens on integrative governance," Social Science & Medicine, Elsevier, vol. 348(C).
- Aarthi Ravikrishnan & Indrik Wijaya & Eileen Png & Kern Rei Chng & Eliza Xin Pei Ho & Amanda Hui Qi Ng & Ahmad Nazri Mohamed Naim & Jean-Sebastien Gounot & Shou Ping Guan & Jasinda Lee Hanqing & Lihua, 2024. "Gut metagenomes of Asian octogenarians reveal metabolic potential expansion and distinct microbial species associated with aging phenotypes," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
- Visanu Thamlikitkul & Surapee Tiengrim & Narisara Thamthaweechok & Preeyanuch Buranapakdee & Wilai Chiemchaisri, 2019. "Contamination by Antibiotic-Resistant Bacteria in Selected Environments in Thailand," IJERPH, MDPI, vol. 16(19), pages 1-11, October.
- Svetlana Kutuzova & Mads Nielsen & Pau Piera & Jakob Nybo Nissen & Simon Rasmussen, 2024. "Taxometer: Improving taxonomic classification of metagenomics contigs," Nature Communications, Nature, vol. 15(1), pages 1-9, December.
- Zi-Teng Liu & Rui-Ao Ma & Dong Zhu & Konstantinos T. Konstantinidis & Yong-Guan Zhu & Si-Yu Zhang, 2024. "Organic fertilization co-selects genetically linked antibiotic and metal(loid) resistance genes in global soil microbiome," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
- Yuxuan Du & Fengzhu Sun, 2023. "MetaCC allows scalable and integrative analyses of both long-read and short-read metagenomic Hi-C data," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
- Zhiguang Qiu & Li Yuan & Chun-Ang Lian & Bin Lin & Jie Chen & Rong Mu & Xuejiao Qiao & Liyu Zhang & Zheng Xu & Lu Fan & Yunzeng Zhang & Shanquan Wang & Junyi Li & Huiluo Cao & Bing Li & Baowei Chen & , 2024. "BASALT refines binning from metagenomic data and increases resolution of genome-resolved metagenomic analysis," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
- Michelle Baker & Xibin Zhang & Alexandre Maciel-Guerra & Kubra Babaarslan & Yinping Dong & Wei Wang & Yujie Hu & David Renney & Longhai Liu & Hui Li & Maqsud Hossain & Stephan Heeb & Zhiqin Tong & Nic, 2024. "Convergence of resistance and evolutionary responses in Escherichia coli and Salmonella enterica co-inhabiting chicken farms in China," Nature Communications, Nature, vol. 15(1), pages 1-21, December.
- Claas Kirchhelle, 2023. "The Antibiocene – towards an eco-social analysis of humanity’s antimicrobial footprint," Palgrave Communications, Palgrave Macmillan, vol. 10(1), pages 1-12, December.
- Zhenghu Zhou & Chuankuan Wang & Xinyu Cha & Tao Zhou & Xuesen Pang & Fazhu Zhao & Xinhui Han & Gaihe Yang & Gehong Wei & Chengjie Ren, 2024. "The biogeography of soil microbiome potential growth rates," Nature Communications, Nature, vol. 15(1), pages 1-9, December.
- Ágnes Becsei & Alessandro Fuschi & Saria Otani & Ravi Kant & Ilja Weinstein & Patricia Alba & József Stéger & Dávid Visontai & Christian Brinch & Miranda Graaf & Claudia M. E. Schapendonk & Antonio Ba, 2024. "Time-series sewage metagenomics distinguishes seasonal, human-derived and environmental microbial communities potentially allowing source-attributed surveillance," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
- Ayse Ercumen & Andrew N. Mertens & Zachary Butzin-Dozier & Da Kyung Jung & Shahjahan Ali & Beryl S. Achando & Gouthami Rao & Caitlin Hemlock & Amy J. Pickering & Christine P. Stewart & Sophia T. Tan &, 2025. "Water, sanitation, handwashing, and nutritional interventions can reduce child antibiotic use: evidence from Bangladesh and Kenya," Nature Communications, Nature, vol. 16(1), pages 1-11, December.
Corrections
All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-57088-y. See general information about how to correct material in RePEc.
If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.
If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .
If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.
For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .
Please note that corrections may take a couple of weeks to filter through the various RePEc services.