Whole Genome Sequencing for Studying Antimicrobial Resistance

Overview

Journal Antibiotics (Basel)

Specialty Pharmacology

Date 2023 Jul 29

PMID 37508231

Authors

Belen Fernandez-Caso

Ana Miqueleiz

Teresa Alarcon

Affiliations

Soon will be listed here.

Abstract

Antibiotic resistance (AMR) is an alarming concern worldwide and , one of the most prevalent bacteria, is not an exception. With antibiotics being its primary therapy, increasing resistance leads to a higher rate of treatment failure. Understanding the genomic mechanisms of resistance to clarithromycin, levofloxacin, metronidazole, amoxicillin, tetracycline, and rifampicin through next-generation sequencing-based molecular tools, such as whole genome sequencing (WGS), can be of great value, not only to direct a patient's treatment, but also to establish and optimize treatment guidelines according to the local epidemiology and to avoid the use of inappropriate antibiotics. WGS approaches allow us to gain insight into the genomic determinants involved in AMR. To this end, different pipelines and platforms are continuously being developed. In this study, we take a more detailed view of the use and progression of WGS for in-depth study of 's AMR.

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References

Aguilera-Correa J, Urruzuno P, Barrio J, Martinez M, Agudo S, Somodevilla A . Detection of Helicobacter pylori and the genotypes of resistance to clarithromycin and the heterogeneous genotype to this antibiotic in biopsies obtained from symptomatic children. Diagn Microbiol Infect Dis. 2016; 87(2):150-153. DOI: 10.1016/j.diagmicrobio.2016.03.001. View

Boyce K . Mutators Enhance Adaptive Micro-Evolution in Pathogenic Microbes. Microorganisms. 2022; 10(2). PMC: 8875331. DOI: 10.3390/microorganisms10020442. View

Savoldi A, Carrara E, Graham D, Conti M, Tacconelli E . Prevalence of Antibiotic Resistance in Helicobacter pylori: A Systematic Review and Meta-analysis in World Health Organization Regions. Gastroenterology. 2018; 155(5):1372-1382.e17. PMC: 6905086. DOI: 10.1053/j.gastro.2018.07.007. View

Park S, Kim J . Trends in Next-Generation Sequencing and a New Era for Whole Genome Sequencing. Int Neurourol J. 2016; 20(Suppl 2):S76-83. PMC: 5169091. DOI: 10.5213/inj.1632742.371. View

Boyanova L, Hadzhiyski P, Gergova R, Markovska R . Evolution of Resistance to Antibiotics: A Topic of Increasing Concern. Antibiotics (Basel). 2023; 12(2). PMC: 9952372. DOI: 10.3390/antibiotics12020332. View

Seriki A, Smith S, Adeleye A, Fowora M . Molecular analysis of low-level tetracycline resistance in clinical isolates of Helicobacter pylori among dyspeptic patients in South West Nigeria. J Glob Antimicrob Resist. 2018; 13:143-145. DOI: 10.1016/j.jgar.2018.01.003. View

Olson R, Assaf R, Brettin T, Conrad N, Cucinell C, Davis J . Introducing the Bacterial and Viral Bioinformatics Resource Center (BV-BRC): a resource combining PATRIC, IRD and ViPR. Nucleic Acids Res. 2022; 51(D1):D678-D689. PMC: 9825582. DOI: 10.1093/nar/gkac1003. View

Tshibangu-Kabamba E, Ngoma-Kisoko P, Tuan V, Matsumoto T, Akada J, Kido Y . Next-Generation Sequencing of the Whole Bacterial Genome for Tracking Molecular Insight into the Broad-Spectrum Antimicrobial Resistance of Clinical Isolates from the Democratic Republic of Congo. Microorganisms. 2020; 8(6). PMC: 7356661. DOI: 10.3390/microorganisms8060887. View

Liu M, Chen H, Gao D, Ma C, Zhang Z . Identification of Membrane Proteins Using Sequence-Based Features. Comput Math Methods Med. 2022; 2022:7493834. PMC: 8769816. DOI: 10.1155/2022/7493834. View

10.

Wang Y, Gong X, Liu D, Zeng R, Zhou L, Sun X . Characteristics of Heteroresistance in Gastric Biopsies and Its Clinical Relevance. Front Cell Infect Microbiol. 2022; 11:819506. PMC: 8855363. DOI: 10.3389/fcimb.2021.819506. View

11.

Heep M, Beck D, Bayerdorffer E, Lehn N . Rifampin and rifabutin resistance mechanism in Helicobacter pylori. Antimicrob Agents Chemother. 1999; 43(6):1497-9. PMC: 89306. DOI: 10.1128/AAC.43.6.1497. View

12.

Dorer M, Sessler T, Salama N . Recombination and DNA repair in Helicobacter pylori. Annu Rev Microbiol. 2011; 65:329-48. PMC: 3743418. DOI: 10.1146/annurev-micro-090110-102931. View

13.

Saracino I, Pavoni M, Zullo A, Fiorini G, Lazzarotto T, Borghi C . Next Generation Sequencing for the Prediction of the Antibiotic Resistance in : A Literature Review. Antibiotics (Basel). 2021; 10(4). PMC: 8070836. DOI: 10.3390/antibiotics10040437. View

14.

Chen J, Ye L, Jin L, Xu X, Xu P, Wang X . Application of next-generation sequencing to characterize novel mutations in clarithromycin-susceptible Helicobacter pylori strains with A2143G of 23S rRNA gene. Ann Clin Microbiol Antimicrob. 2018; 17(1):10. PMC: 5863438. DOI: 10.1186/s12941-018-0259-8. View

15.

Liu Y, Wang S, Yang F, Chi W, Ding L, Liu T . Antimicrobial resistance patterns and genetic elements associated with the antibiotic resistance of Helicobacter pylori strains from Shanghai. Gut Pathog. 2022; 14(1):14. PMC: 8966258. DOI: 10.1186/s13099-022-00488-y. View

16.

Marques A, Vitor J, Santos A, Oleastro M, Vale F . Trends in resistance to clarithromycin: from phenotypic to genomic approaches. Microb Genom. 2020; 6(3). PMC: 7200067. DOI: 10.1099/mgen.0.000344. View

17.

Ferrer Florensa A, Kaas R, Clausen P, Aytan-Aktug D, Aarestrup F . ResFinder - an open online resource for identification of antimicrobial resistance genes in next-generation sequencing data and prediction of phenotypes from genotypes. Microb Genom. 2022; 8(1). PMC: 8914360. DOI: 10.1099/mgen.0.000748. View

18.

Uelze L, Grutzke J, Borowiak M, Hammerl J, Juraschek K, Deneke C . Typing methods based on whole genome sequencing data. One Health Outlook. 2021; 2:3. PMC: 7993478. DOI: 10.1186/s42522-020-0010-1. View

19.

Argueta E, Ho J, Elfanagely Y, DAgata E, Moss S . Clinical Implication of Drug Resistance for Management. Antibiotics (Basel). 2022; 11(12). PMC: 9774604. DOI: 10.3390/antibiotics11121684. View

20.

Rimbara E, Noguchi N, Kawai T, Sasatsu M . Mutations in penicillin-binding proteins 1, 2 and 3 are responsible for amoxicillin resistance in Helicobacter pylori. J Antimicrob Chemother. 2008; 61(5):995-8. DOI: 10.1093/jac/dkn051. View