Besides phenotypic antimicrobial susceptibility testing (AST), whole genome sequencing (WGS) is a promising alternative approach for detection of resistance phenotypes. The aim of this study was to investigate the concordance between WGS-based resistance prediction and phenotypic AST results for enterococcal clinical isolates using a user-friendly online tools and databases. A total of 172 clinical isolates (34 E. faecalis, 138 E. faecium) received at the French National Reference Center for enterococci from 2017 to 2020 were included. AST was performed by disc diffusion or MIC determination for 14 antibiotics according to CA-SFM/EUCAST guidelines. The genome of all strains was sequenced using the Illumina technology (MiSeq) with bioinformatic analysis from raw reads using online tools ResFinder 4.1 and LRE-finder 1.0. For both E. faecalis and E. faecium, performances of WGS-based genotype to predict resistant phenotypes were excellent (concordance > 90%), particularly for antibiotics commonly used for treatment of enterococcal infections such as ampicillin, gentamicin, vancomycin, teicoplanin, and linezolid. Note that 100% very major errors were found for quinupristin-dalfopristin, tigecycline, and rifampicin for which resistance mutations are not included in databases. Also, it was not possible to predict phenotype from genotype for daptomycin for the same reason. WGS combined with online tools could be easily used by non-expert clinical microbiologists as a rapid and reliable tool for prediction of phenotypic resistance to first-line antibiotics among enterococci. Nonetheless, some improvements should be made such as the implementation of resistance mutations in the database for some antibiotics.
This is a preview of subscription content, access via your institution.
Buy single article
Instant access to the full article PDF.
Price excludes VAT (USA)
Tax calculation will be finalised during checkout.
The genomic datasets generated and analyzed during the current study are available in GenBank as bioproject PRJNA875074.
Cattoir V (2022) The multifaceted lifestyle of enterococci: genetic diversity, ecology and risks for public health. Curr Opin Microbiol 65:73–80
Arias CA, Murray BE (2012) The rise of the Enterococcus: beyond vancomycin resistance. Nat Rev Microbiol 10(4):266–278
Bender JK, Cattoir V, Hegstad K, Sadowy E, Coque TM, Westh H et al (2018) Update on prevalence and mechanisms of resistance to linezolid, tigecycline and daptomycin in enterococci in Europe: Towards a common nomenclature. Drug Resist Updat 40:25–39
García-Solache M, Rice LB (2019) The Enterococcus: a model of adaptability to its environment. Clin Microbiol Rev 32(2):e00058-e118
Wheat PF (2001) History and development of antimicrobial susceptibility testing methodology. J Antimicrob Chemother 48(Suppl 1):1–4
Khan ZA, Siddiqui MF, Park S (2019) Current and emerging methods of antibiotic susceptibility testing. Diagnostics 9(2):49
Stoesser N, Batty EM, Eyre DW, Morgan M, Wyllie DH, Del Ojo EC et al (2013) Predicting antimicrobial susceptibilities for Escherichia coli and Klebsiella pneumoniae isolates using whole genomic sequence data. J Antimicrob Chemother 68(10):2234–2244
Gordon NC, Price JR, Cole K, Everitt R, Morgan M, Finney J et al (2014) Prediction of Staphylococcus aureus antimicrobial resistance by whole-genome sequencing. J Clin Microbiol 52(4):1182–1191
Tyson GH, McDermott PF, Li C, Chen Y, Tadesse DA, Mukherjee S et al (2015) WGS accurately predicts antimicrobial resistance in Escherichia coli. J Antimicrob Chemother 70(10):2763–2769
Bradley P, Gordon NC, Walker TM, Dunn L, Heys S, Huang B et al (2015) Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis. Nat Commun 6(1):10063
McDermott PF, Tyson GH, Kabera C, Chen Y, Li C, Folster JP et al (2016) Whole-genome sequencing for detecting antimicrobial resistance in nontyphoidal Salmonella. Antimicrob Agents Chemother 60(9):5515–5520
Ruppé E, Cherkaoui A, Charretier Y, Girard M, Schicklin S, Lazarevic V et al (2020) From genotype to antibiotic susceptibility phenotype in the order Enterobacterales: a clinical perspective. Clin Microbiol Infect 26(5):643
Dahl LG, Joensen KG, Østerlund MT, Kiil K, Nielsen EM (2021) Prediction of antimicrobial resistance in clinical Campylobacter jejuni isolates from whole-genome sequencing data. Eur J Clin Microbiol Infect Dis 40(4):673–682
Cortes-Lara S, Barrio-Tofiño ED, López-Causapé C, Oliver A, GEMARA-SEIMC/REIPI Pseudomonas study Group (2021) Predicting Pseudomonas aeruginosa susceptibility phenotypes from whole genome sequence resistome analysis. Clin Microbiol Infect 27(11):1631–1637
Anjum MF, Zankari E, Hasman H (2017) Molecular methods for detection of antimicrobial resistance. Microbiol Spectr 5(6). https://doi.org/10.1128/microbiolspec.ARBA-0011-2017
Su M, Satola SW, Read TD (2019) Genome-based prediction of bacterial antibiotic resistance. J Clin Microbiol 57(3):e01405-e1418
Papp M, Solymosi N (2022) Review and comparison of antimicrobial resistance gene databases. Antibiot (Basel) 11(3):339
Zankari E, Hasman H, Cosentino S, Vestergaard M, Rasmussen S, Lund O et al (2012) Identification of acquired antimicrobial resistance genes. J Antimicrob Chemother 67(11):2640–2644
Florensa AF, Kaas RS, Clausen PTLC, Aytan-Aktug D, Aarestrup FM (2022) ResFinder — an open online resource for identification of antimicrobial resistance genes in next-generation sequencing data and prediction of phenotypes from genotypes. Microb Genomics 8(1):000748
Bortolaia V, Kaas RS, Ruppe E, Roberts MC, Schwarz S, Cattoir V et al (2020) ResFinder 4.0 for predictions of phenotypes from genotypes. J Antimicrob Chemother 75(12):3491–3500
Zankari E, Allesøe R, Joensen KG, Cavaco LM, Lund O, Aarestrup FM (2017) PointFinder: a novel web tool for WGS-based detection of antimicrobial resistance associated with chromosomal point mutations in bacterial pathogens. J Antimicrob Chemother 72(10):2764–2768
Clausen PTLC, Aarestrup FM, Lund O (2018) Rapid and precise alignment of raw reads against redundant databases with KMA. BMC Bioinformatics 19(1):307
Hasman H, Clausen PTLC, Kaya H, Hansen F, Knudsen JD, Wang M et al (2019) LRE-Finder, a Web tool for detection of the 23S rRNA mutations and the optrA, cfr, cfr(B) and poxtA genes encoding linezolid resistance in enterococci from whole-genome sequences. J Antimicrob Chemother 74(6):1473–1476
Zankari E, Hasman H, Kaas RS, Seyfarth AM, Agersø Y, Lund O et al (2013) Genotyping using whole-genome sequencing is a realistic alternative to surveillance based on phenotypic antimicrobial susceptibility testing. J Antimicrob Chemother 68(4):771–777
Tyson GH, Sabo JL, Rice-Trujillo C, Hernandez J, McDermott PF (2018) Whole-genome sequencing based characterization of antimicrobial resistance in Enterococcus. Pathog Dis 76(2):fty018
Babiker A, Mustapha MM, Pacey MP, Shutt KA, Ezeonwuka CD, Ohm SL et al (2019) Use of online tools for antimicrobial resistance prediction by whole-genome sequencing in methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant enterococci (VRE). J Glob Antimicrob Resist 19:136–143
Anahtar MN, Bramante JT, Xu J, Desrosiers LA, Paer JM, Rosenberg ES et al (2022) Prediction of antimicrobial resistance in clinical Enterococcus faecium isolates using a rules-based analysis of whole-genome sequences. Antimicrob Agents Chemother 66(1):e01196-e1221
Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS et al (2012) SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol J Comput Mol Cell Biol 19(5):455–477
Neumann B, Prior K, Bender JK, Harmsen D, Klare I, Fuchs S et al (2019) A core genome multilocus sequence typing scheme for Enterococcus faecalis. J Clin Microbiol 57(3):e01686-e1718
de Been M, Pinholt M, Top J, Bletz S, Mellmann A, van Schaik W et al (2015) Core genome multilocus sequence typing scheme for high-resolution typing of Enterococcus faecium. J Clin Microbiol 53(12):3788–3797
Letunic I, Bork P (2021) Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Res 49(W1):W293–W296
Singh KV, Weinstock GM, Murray BE (2002) An Enterococcus faecalis ABC homologue (Lsa) is required for the resistance of this species to clindamycin and quinupristin-dalfopristin. Antimicrob Agents Chemother 46(6):1845–1850
Cattoir V, Isnard C, Cosquer T, Odhiambo A, Bucquet F, Guérin F et al (2015) Genomic analysis of reduced susceptibility to tigecycline in Enterococcus faecium. Antimicrob Agents Chemother 59(1):239–244
Isnard C, Malbruny B, Leclercq R, Cattoir V (2013) Genetic basis for in vitro and in vivo resistance to lincosamides, streptogramins A, and pleuromutilins (LSAP phenotype) in Enterococcus faecium. Antimicrob Agents Chemother 57(9):4463–4469
This work was supported by “Santé Publique France,” the French national public health agency.
Consent to participate
Consent for publication
Conflict of interest
The authors declare no competing interests.
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Genetic relationship and resistance gene content among 34 E. faecalis clinical isolates. Neighbor-joining phylogenetic tree was constructed from aligned core-genome SNPs analysis based on SNPs and visualized together with ST affiliation (colored strips) and a heatmap for resistance mechanisms (black boxes) with iTOL v5. The scale bar represents 100 SNPs. (PNG 405 kb)
Genetic relationship and resistance gene content among 138 E. faecium clinical isolates. Neighbor-joining phylogenetic tree was constructed from aligned core-genome SNPs analysis based on SNPs and visualized together with ST affiliation (colored strips) and a heatmap for resistance mechanisms (black boxes) with iTOL v5. The scale bar represents 1,000 SNPs. (PNG 914 kb)
About this article
Cite this article
Penven, M., Zouari, A., Nogues, S. et al. Web-based prediction of antimicrobial resistance in enterococcal clinical isolates by whole-genome sequencing. Eur J Clin Microbiol Infect Dis 42, 67–76 (2023). https://doi.org/10.1007/s10096-022-04527-z