Research
Print page Print page
Switch language
The Capital Region of Denmark - a part of Copenhagen University Hospital
Published

ResFinder 4.0 for predictions of phenotypes from genotypes

Research output: Contribution to journalJournal articleResearchpeer-review

Harvard

Bortolaia, V, Kaas, RS, Ruppe, E, Roberts, MC, Schwarz, S, Cattoir, V, Philippon, A, Allesoe, RL, Rebelo, AR, Florensa, AF, Fagelhauer, L, Chakraborty, T, Neumann, B, Werner, G, Bender, JK, Stingl, K, Nguyen, M, Coppens, J, Xavier, BB, Malhotra-Kumar, S, Westh, H, Pinholt, M, Anjum, MF, Duggett, NA, Kempf, I, Nykäsenoja, S, Olkkola, S, Wieczorek, K, Amaro, A, Clemente, L, Mossong, J, Losch, S, Ragimbeau, C, Lund, O & Aarestrup, FM 2020, 'ResFinder 4.0 for predictions of phenotypes from genotypes', The Journal of antimicrobial chemotherapy, vol. 75, no. 12, pp. 3491-3500. https://doi.org/10.1093/jac/dkaa345

APA

Bortolaia, V., Kaas, R. S., Ruppe, E., Roberts, M. C., Schwarz, S., Cattoir, V., Philippon, A., Allesoe, R. L., Rebelo, A. R., Florensa, A. F., Fagelhauer, L., Chakraborty, T., Neumann, B., Werner, G., Bender, J. K., Stingl, K., Nguyen, M., Coppens, J., Xavier, B. B., ... Aarestrup, F. M. (2020). ResFinder 4.0 for predictions of phenotypes from genotypes. The Journal of antimicrobial chemotherapy, 75(12), 3491-3500. https://doi.org/10.1093/jac/dkaa345

CBE

Bortolaia V, Kaas RS, Ruppe E, Roberts MC, Schwarz S, Cattoir V, Philippon A, Allesoe RL, Rebelo AR, Florensa AF, Fagelhauer L, Chakraborty T, Neumann B, Werner G, Bender JK, Stingl K, Nguyen M, Coppens J, Xavier BB, Malhotra-Kumar S, Westh H, Pinholt M, Anjum MF, Duggett NA, Kempf I, Nykäsenoja S, Olkkola S, Wieczorek K, Amaro A, Clemente L, Mossong J, Losch S, Ragimbeau C, Lund O, Aarestrup FM. 2020. ResFinder 4.0 for predictions of phenotypes from genotypes. The Journal of antimicrobial chemotherapy. 75(12):3491-3500. https://doi.org/10.1093/jac/dkaa345

MLA

Vancouver

Bortolaia V, Kaas RS, Ruppe E, Roberts MC, Schwarz S, Cattoir V et al. ResFinder 4.0 for predictions of phenotypes from genotypes. The Journal of antimicrobial chemotherapy. 2020 Dec 1;75(12):3491-3500. https://doi.org/10.1093/jac/dkaa345

Author

Bortolaia, Valeria ; Kaas, Rolf S ; Ruppe, Etienne ; Roberts, Marilyn C ; Schwarz, Stefan ; Cattoir, Vincent ; Philippon, Alain ; Allesoe, Rosa L ; Rebelo, Ana Rita ; Florensa, Alfred Ferrer ; Fagelhauer, Linda ; Chakraborty, Trinad ; Neumann, Bernd ; Werner, Guido ; Bender, Jennifer K ; Stingl, Kerstin ; Nguyen, Minh ; Coppens, Jasmine ; Xavier, Basil Britto ; Malhotra-Kumar, Surbhi ; Westh, Henrik ; Pinholt, Mette ; Anjum, Muna F ; Duggett, Nicholas A ; Kempf, Isabelle ; Nykäsenoja, Suvi ; Olkkola, Satu ; Wieczorek, Kinga ; Amaro, Ana ; Clemente, Lurdes ; Mossong, Joël ; Losch, Serge ; Ragimbeau, Catherine ; Lund, Ole ; Aarestrup, Frank M. / ResFinder 4.0 for predictions of phenotypes from genotypes. In: The Journal of antimicrobial chemotherapy. 2020 ; Vol. 75, No. 12. pp. 3491-3500.

Bibtex

@article{0e7739872bfa4a33a28eff057cf35b3d,
title = "ResFinder 4.0 for predictions of phenotypes from genotypes",
abstract = "Objectives: WGS-based antimicrobial susceptibility testing (AST) is as reliable as phenotypic AST for several antimicrobial/bacterial species combinations. However, routine use of WGS-based AST is hindered by the need for bioinformatics skills and knowledge of antimicrobial resistance (AMR) determinants to operate the vast majority of tools developed to date. By leveraging on ResFinder and PointFinder, two freely accessible tools that can also assist users without bioinformatics skills, we aimed at increasing their speed and providing an easily interpretable antibiogram as output. Methods: The ResFinder code was re-written to process raw reads and use Kmer-based alignment. The existing ResFinder and PointFinder databases were revised and expanded. Additional databases were developed including a genotype-to-phenotype key associating each AMR determinant with a phenotype at the antimicrobial compound level, and species-specific panels for in silico antibiograms. ResFinder 4.0 was validated using Escherichia coli (n = 584), Salmonella spp. (n = 1081), Campylobacter jejuni (n = 239), Enterococcus faecium (n = 106), Enterococcus faecalis (n = 50) and Staphylococcus aureus (n = 163) exhibiting different AST profiles, and from different human and animal sources and geographical origins. Results: Genotype-phenotype concordance was ≥95% for 46/51 and 25/32 of the antimicrobial/species combinations evaluated for Gram-negative and Gram-positive bacteria, respectively. When genotype-phenotype concordance was <95%, discrepancies were mainly linked to criteria for interpretation of phenotypic tests and suboptimal sequence quality, and not to ResFinder 4.0 performance. Conclusions: WGS-based AST using ResFinder 4.0 provides in silico antibiograms as reliable as those obtained by phenotypic AST at least for the bacterial species/antimicrobial agents of major public health relevance considered.",
author = "Valeria Bortolaia and Kaas, {Rolf S} and Etienne Ruppe and Roberts, {Marilyn C} and Stefan Schwarz and Vincent Cattoir and Alain Philippon and Allesoe, {Rosa L} and Rebelo, {Ana Rita} and Florensa, {Alfred Ferrer} and Linda Fagelhauer and Trinad Chakraborty and Bernd Neumann and Guido Werner and Bender, {Jennifer K} and Kerstin Stingl and Minh Nguyen and Jasmine Coppens and Xavier, {Basil Britto} and Surbhi Malhotra-Kumar and Henrik Westh and Mette Pinholt and Anjum, {Muna F} and Duggett, {Nicholas A} and Isabelle Kempf and Suvi Nyk{\"a}senoja and Satu Olkkola and Kinga Wieczorek and Ana Amaro and Lurdes Clemente and Jo{\"e}l Mossong and Serge Losch and Catherine Ragimbeau and Ole Lund and Aarestrup, {Frank M}",
note = "{\textcopyright} The Author(s) 2020. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy.",
year = "2020",
month = dec,
day = "1",
doi = "10.1093/jac/dkaa345",
language = "English",
volume = "75",
pages = "3491--3500",
journal = "Journal of Antimicrobial Chemotherapy",
issn = "0305-7453",
publisher = "Oxford University Press",
number = "12",

}

RIS

TY - JOUR

T1 - ResFinder 4.0 for predictions of phenotypes from genotypes

AU - Bortolaia, Valeria

AU - Kaas, Rolf S

AU - Ruppe, Etienne

AU - Roberts, Marilyn C

AU - Schwarz, Stefan

AU - Cattoir, Vincent

AU - Philippon, Alain

AU - Allesoe, Rosa L

AU - Rebelo, Ana Rita

AU - Florensa, Alfred Ferrer

AU - Fagelhauer, Linda

AU - Chakraborty, Trinad

AU - Neumann, Bernd

AU - Werner, Guido

AU - Bender, Jennifer K

AU - Stingl, Kerstin

AU - Nguyen, Minh

AU - Coppens, Jasmine

AU - Xavier, Basil Britto

AU - Malhotra-Kumar, Surbhi

AU - Westh, Henrik

AU - Pinholt, Mette

AU - Anjum, Muna F

AU - Duggett, Nicholas A

AU - Kempf, Isabelle

AU - Nykäsenoja, Suvi

AU - Olkkola, Satu

AU - Wieczorek, Kinga

AU - Amaro, Ana

AU - Clemente, Lurdes

AU - Mossong, Joël

AU - Losch, Serge

AU - Ragimbeau, Catherine

AU - Lund, Ole

AU - Aarestrup, Frank M

N1 - © The Author(s) 2020. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy.

PY - 2020/12/1

Y1 - 2020/12/1

N2 - Objectives: WGS-based antimicrobial susceptibility testing (AST) is as reliable as phenotypic AST for several antimicrobial/bacterial species combinations. However, routine use of WGS-based AST is hindered by the need for bioinformatics skills and knowledge of antimicrobial resistance (AMR) determinants to operate the vast majority of tools developed to date. By leveraging on ResFinder and PointFinder, two freely accessible tools that can also assist users without bioinformatics skills, we aimed at increasing their speed and providing an easily interpretable antibiogram as output. Methods: The ResFinder code was re-written to process raw reads and use Kmer-based alignment. The existing ResFinder and PointFinder databases were revised and expanded. Additional databases were developed including a genotype-to-phenotype key associating each AMR determinant with a phenotype at the antimicrobial compound level, and species-specific panels for in silico antibiograms. ResFinder 4.0 was validated using Escherichia coli (n = 584), Salmonella spp. (n = 1081), Campylobacter jejuni (n = 239), Enterococcus faecium (n = 106), Enterococcus faecalis (n = 50) and Staphylococcus aureus (n = 163) exhibiting different AST profiles, and from different human and animal sources and geographical origins. Results: Genotype-phenotype concordance was ≥95% for 46/51 and 25/32 of the antimicrobial/species combinations evaluated for Gram-negative and Gram-positive bacteria, respectively. When genotype-phenotype concordance was <95%, discrepancies were mainly linked to criteria for interpretation of phenotypic tests and suboptimal sequence quality, and not to ResFinder 4.0 performance. Conclusions: WGS-based AST using ResFinder 4.0 provides in silico antibiograms as reliable as those obtained by phenotypic AST at least for the bacterial species/antimicrobial agents of major public health relevance considered.

AB - Objectives: WGS-based antimicrobial susceptibility testing (AST) is as reliable as phenotypic AST for several antimicrobial/bacterial species combinations. However, routine use of WGS-based AST is hindered by the need for bioinformatics skills and knowledge of antimicrobial resistance (AMR) determinants to operate the vast majority of tools developed to date. By leveraging on ResFinder and PointFinder, two freely accessible tools that can also assist users without bioinformatics skills, we aimed at increasing their speed and providing an easily interpretable antibiogram as output. Methods: The ResFinder code was re-written to process raw reads and use Kmer-based alignment. The existing ResFinder and PointFinder databases were revised and expanded. Additional databases were developed including a genotype-to-phenotype key associating each AMR determinant with a phenotype at the antimicrobial compound level, and species-specific panels for in silico antibiograms. ResFinder 4.0 was validated using Escherichia coli (n = 584), Salmonella spp. (n = 1081), Campylobacter jejuni (n = 239), Enterococcus faecium (n = 106), Enterococcus faecalis (n = 50) and Staphylococcus aureus (n = 163) exhibiting different AST profiles, and from different human and animal sources and geographical origins. Results: Genotype-phenotype concordance was ≥95% for 46/51 and 25/32 of the antimicrobial/species combinations evaluated for Gram-negative and Gram-positive bacteria, respectively. When genotype-phenotype concordance was <95%, discrepancies were mainly linked to criteria for interpretation of phenotypic tests and suboptimal sequence quality, and not to ResFinder 4.0 performance. Conclusions: WGS-based AST using ResFinder 4.0 provides in silico antibiograms as reliable as those obtained by phenotypic AST at least for the bacterial species/antimicrobial agents of major public health relevance considered.

UR - http://www.scopus.com/inward/record.url?scp=85092033198&partnerID=8YFLogxK

U2 - 10.1093/jac/dkaa345

DO - 10.1093/jac/dkaa345

M3 - Journal article

C2 - 32780112

VL - 75

SP - 3491

EP - 3500

JO - Journal of Antimicrobial Chemotherapy

JF - Journal of Antimicrobial Chemotherapy

SN - 0305-7453

IS - 12

ER -

ID: 60645572