ResFinder 4.0 contains four databases including AMR genes (ResFinder), chromosomal gene mutations mediating AMR (PointFinder), translation of genotypes into phenotypes and species-specific panels for
in silico antibiograms. The databases of ResFinder
15 (
link) and PointFinder
16 (
link) were reviewed by experts and, when necessary, entries were removed or added. Furthermore, the PointFinder database was extended to include chromosomal gene mutations leading to ampicillin resistance in
Enterococcus faecium, ciprofloxacin resistance in
E. faecium and
Enterococcus faecalis, and resistance to cefoxitin, chloramphenicol, ciprofloxacin, fusidic acid, linezolid, mupirocin, quinupristin–dalfopristin, rifampicin and trimethoprim in
Staphylococcus aureus. The genotype-to-phenotype tables were created by experts, by using additional databases (
www.bldb.eu for β-lactam resistance genes,
18 (
link)
http://faculty.washington.edu/marilynr/ for tetracycline as well as macrolide, lincosamide, streptogramin and oxazolidinone resistance genes) and by performing extensive literature searches. In the genotype-to-phenotype tables, the ResFinder and PointFinder entries have been associated with an AMR phenotype both at the antimicrobial class and at the antimicrobial compound level. A selection of antimicrobial compounds within each class was made to include antimicrobial agents important for clinical and surveillance purposes for the different bacterial species included (Table
S1, available as
Supplementary data at
JAC Online). The genotype-to-phenotype tables also include: (i) the PubMed ID of relevant literature describing the respective AMR determinants and phenotypes, when available; (ii) the mechanism of resistance by which each AMR determinant functions; and (iii) notes, which may contain different information such as warnings on variable expression levels (inducible resistance, cryptic genes in some species, etc.), structural and functional information, and alternative nomenclature.
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., Malhotra-Kumar S., Westh H., Pinholt M., Anjum M.F., Duggett N.A., Kempf I., Nykäsenoja S., Olkkola S., Wieczorek K., Amaro A., Clemente L., Mossong J., Losch S., Ragimbeau C., Lund O, & Aarestrup F.M. (2020). ResFinder 4.0 for predictions of phenotypes from genotypes. Journal of Antimicrobial Chemotherapy, 75(12), 3491-3500.