Antibiotic Resistance: Global Health Crisis and Metagenomics

Overview

Journal Biotechnol Rep (Amst)

Specialty Biotechnology

Date 2021 Mar 18

PMID 33732632

Citations 32

Authors

Shailendra Yadav

Atya Kapley

Affiliations

Soon will be listed here.

Abstract

Antibiotic resistance is a global problem which affects human health. The imprudent use of antibiotics (medicine, agriculture, aquaculture, and food industry) has resulted in the broader dissemination of resistance. Urban wastewater & sewage treatment plants act as the hotspot for the widespread of antimicrobial resistance. Natural environment also plays an important role in the dissemination of resistance. Mapping of antibiotic resistance genes (ARGS) in environment is essential for mitigating antimicrobial resistance (AMR) widespread. Therefore, the review article emphasizes on the application of metagenomics for the surveillance of antimicrobial resistance. Metagenomics is the next generation tool which is being used for cataloging the resistome of diverse environments. We summarize the different metagenomic tools that can be used for mining of ARGs and acquired AMR present in the metagenomic data. Also, we recommend application of targeted sequencing/ capture platform for mapping of resistome with higher specificity and selectivity.

Citing Articles

Metagenomic Analysis of Microbial Community Associated with Food Waste Composting.

Andraskar J, Khan D, Yadav S, Kapley A Appl Biochem Biotechnol. 2025; .

PMID: 39961944 DOI: 10.1007/s12010-025-05203-6.

Phytochemical and Biological Investigations of Crude Extracts of .

Aydemir E, Odabas Kose E, Ozkaya Gul S, Korkut A, Kilit A, Celep M Pharmaceuticals (Basel). 2025; 18(1).

PMID: 39861073 PMC: 11768461. DOI: 10.3390/ph18010010.

Impact of urbanization on antimicrobial resistance in soil microbial communities.

Bongiovanni D, Masson S, Chialva M, Fiorilli V, Votta C, Lanfranco L Sci Rep. 2025; 15(1):633.

PMID: 39753861 PMC: 11698744. DOI: 10.1038/s41598-024-84945-5.

Small molecules targeting the eubacterial β-sliding clamp discovered by combined and screening approaches.

Caputo A, Elisi G, Levati E, Barotti G, Sartini S, Wagner J J Enzyme Inhib Med Chem. 2025; 40(1):2440861.

PMID: 39749973 PMC: 11703123. DOI: 10.1080/14756366.2024.2440861.

Compounds Containing 2,3-Bis(phenylamino) Quinoxaline Exhibit Activity Against Methicillin-Resistant Staphylococcus aureus, Enterococcus faecalis, and Their Biofilms.

Padalino G, Duggan K, Mur L, Maillard J, Brancale A, Hoffmann K Microbiologyopen. 2024; 13(6):e011.

PMID: 39665231 PMC: 11635387. DOI: 10.1002/mbo3.70011.

References

Lok C . Mining the microbial dark matter. Nature. 2015; 522(7556):270-3. DOI: 10.1038/522270a. View

Yang Y, Jiang X, Chai B, Ma L, Li B, Zhang A . ARGs-OAP: online analysis pipeline for antibiotic resistance genes detection from metagenomic data using an integrated structured ARG-database. Bioinformatics. 2016; 32(15):2346-51. DOI: 10.1093/bioinformatics/btw136. View

Blin K, Wolf T, Chevrette M, Lu X, Schwalen C, Kautsar S . antiSMASH 4.0-improvements in chemistry prediction and gene cluster boundary identification. Nucleic Acids Res. 2017; 45(W1):W36-W41. PMC: 5570095. DOI: 10.1093/nar/gkx319. View

Soucy S, Huang J, Gogarten J . Horizontal gene transfer: building the web of life. Nat Rev Genet. 2015; 16(8):472-82. DOI: 10.1038/nrg3962. View

Nichols D, Cahoon N, Trakhtenberg E, Pham L, Mehta A, Belanger A . Use of ichip for high-throughput in situ cultivation of "uncultivable" microbial species. Appl Environ Microbiol. 2010; 76(8):2445-50. PMC: 2849220. DOI: 10.1128/AEM.01754-09. View

Yadav S, Kapley A . Exploration of activated sludge resistome using metagenomics. Sci Total Environ. 2019; 692:1155-1164. DOI: 10.1016/j.scitotenv.2019.07.267. View

von Wintersdorff C, Penders J, van Niekerk J, Mills N, Majumder S, van Alphen L . Dissemination of Antimicrobial Resistance in Microbial Ecosystems through Horizontal Gene Transfer. Front Microbiol. 2016; 7:173. PMC: 4759269. DOI: 10.3389/fmicb.2016.00173. View

Banik J, Brady S . Recent application of metagenomic approaches toward the discovery of antimicrobials and other bioactive small molecules. Curr Opin Microbiol. 2010; 13(5):603-9. PMC: 3111150. DOI: 10.1016/j.mib.2010.08.012. View

Beceiro A, Tomas M, Bou G . Antimicrobial resistance and virulence: a successful or deleterious association in the bacterial world?. Clin Microbiol Rev. 2013; 26(2):185-230. PMC: 3623377. DOI: 10.1128/CMR.00059-12. View

10.

Gupta S, Padmanabhan B, Diene S, Lopez-Rojas R, Kempf M, Landraud L . ARG-ANNOT, a new bioinformatic tool to discover antibiotic resistance genes in bacterial genomes. Antimicrob Agents Chemother. 2013; 58(1):212-20. PMC: 3910750. DOI: 10.1128/AAC.01310-13. View

11.

Gonzalez-Plaza J, Blau K, Milakovic M, Jurina T, Smalla K, Udikovic-Kolic N . Antibiotic-manufacturing sites are hot-spots for the release and spread of antibiotic resistance genes and mobile genetic elements in receiving aquatic environments. Environ Int. 2019; 130:104735. DOI: 10.1016/j.envint.2019.04.007. View

12.

Wellington E, Boxall A, Cross P, Feil E, Gaze W, Hawkey P . The role of the natural environment in the emergence of antibiotic resistance in gram-negative bacteria. Lancet Infect Dis. 2013; 13(2):155-65. DOI: 10.1016/S1473-3099(12)70317-1. View

13.

Brockhurst M, Harrison F, Veening J, Harrison E, Blackwell G, Iqbal Z . Assessing evolutionary risks of resistance for new antimicrobial therapies. Nat Ecol Evol. 2019; 3(4):515-517. DOI: 10.1038/s41559-019-0854-x. View

14.

McGarvey K, Queitsch K, Fields S . Wide variation in antibiotic resistance proteins identified by functional metagenomic screening of a soil DNA library. Appl Environ Microbiol. 2012; 78(6):1708-14. PMC: 3298129. DOI: 10.1128/AEM.06759-11. View

15.

Brunton L, Desbois A, Garza M, Wieland B, Mohan C, Hasler B . Identifying hotspots for antibiotic resistance emergence and selection, and elucidating pathways to human exposure: Application of a systems-thinking approach to aquaculture systems. Sci Total Environ. 2019; 687:1344-1356. PMC: 6905156. DOI: 10.1016/j.scitotenv.2019.06.134. View

16.

Inouye M, Dashnow H, Raven L, Schultz M, Pope B, Tomita T . SRST2: Rapid genomic surveillance for public health and hospital microbiology labs. Genome Med. 2014; 6(11):90. PMC: 4237778. DOI: 10.1186/s13073-014-0090-6. View

17.

Pouwels K, Chatterjee A, Cooper B, Robotham J . Antibiotic resistance, stewardship, and consumption. Lancet Planet Health. 2019; 3(2):e66. DOI: 10.1016/S2542-5196(18)30283-3. View

18.

Mendelson M, Matsoso M . The World Health Organization Global Action Plan for antimicrobial resistance. S Afr Med J. 2015; 105(5):325. DOI: 10.7196/samj.9644. View

19.

Chait R, Vetsigian K, Kishony R . What counters antibiotic resistance in nature?. Nat Chem Biol. 2011; 8(1):2-5. DOI: 10.1038/nchembio.745. View

20.

Rowe W, Baker K, Verner-Jeffreys D, Baker-Austin C, Ryan J, Maskell D . Search Engine for Antimicrobial Resistance: A Cloud Compatible Pipeline and Web Interface for Rapidly Detecting Antimicrobial Resistance Genes Directly from Sequence Data. PLoS One. 2015; 10(7):e0133492. PMC: 4510569. DOI: 10.1371/journal.pone.0133492. View