Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2017 Oct 1;72(10):2764-2768.
doi: 10.1093/jac/dkx217.

PointFinder: A Novel Web Tool for WGS-based Detection of Antimicrobial Resistance Associated With Chromosomal Point Mutations in Bacterial Pathogens

Free PMC article

PointFinder: A Novel Web Tool for WGS-based Detection of Antimicrobial Resistance Associated With Chromosomal Point Mutations in Bacterial Pathogens

Ea Zankari et al. J Antimicrob Chemother. .
Free PMC article


Background: Antibiotic resistance is a major health problem, as drugs that were once highly effective no longer cure bacterial infections. WGS has previously been shown to be an alternative method for detecting horizontally acquired antimicrobial resistance genes. However, suitable bioinformatics methods that can provide easily interpretable, accurate and fast results for antimicrobial resistance associated with chromosomal point mutations are still lacking.

Methods: Phenotypic antimicrobial susceptibility tests were performed on 150 isolates covering three different bacterial species: Salmonella enterica, Escherichia coli and Campylobacter jejuni. The web-server ResFinder-2.1 was used to identify acquired antimicrobial resistance genes and two methods, the novel PointFinder (using BLAST) and an in-house method (mapping of raw WGS reads), were used to identify chromosomal point mutations. Results were compared with phenotypic antimicrobial susceptibility testing results.

Results: A total of 685 different phenotypic tests associated with chromosomal resistance to quinolones, polymyxin, rifampicin, macrolides and tetracyclines resulted in 98.4% concordance. Eleven cases of disagreement between tested and predicted susceptibility were observed: two C. jejuni isolates with phenotypic fluoroquinolone resistance and two with phenotypic erythromycin resistance and five colistin-susceptible E. coli isolates with a detected pmrB V161G mutation when assembled with Velvet, but not when using SPAdes or when mapping the reads.

Conclusions: PointFinder proved, with high concordance between phenotypic and predicted antimicrobial susceptibility, to be a user-friendly web tool for detection of chromosomal point mutations associated with antimicrobial resistance.

Similar articles

See all similar articles

Cited by 29 articles

See all "Cited by" articles


    1. Zankari E, Hasman H, Kaas RS. et al. Genotyping using whole-genome sequencing is a realistic alternative to surveillance based on phenotypic antimicrobial susceptibility testing. J Antimicrob Chemother 2013; 68: 771–7. - PubMed
    1. Stoesser N, Batty EM, Eyre DW. et al. Predicting antimicrobial susceptibilities for Escherichia coli and Klebsiella pneumoniae isolates using whole genomic sequence data. J Antimicrob Chemother 2013; 68: 2234–44. - PMC - PubMed
    1. Bradley P, Gordon NC, Walker TM. et al. Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis. Nat Commun 2015; 6: 10063. - PMC - PubMed
    1. Hopkins KL, Davies RH, Threlfall EJ. Mechanisms of quinolone resistance in Escherichia coli and Salmonella: recent developments. Int J Antimicrob Agents 2005; 25: 358–73. - PubMed
    1. Confreres A, Maxwell A. gyrB mutations which confer coumarin resistance also affect DNA supercoiling and ATP hydrolysis by Escherichia coli DNA gyrase. Mol Microbiol 1992; 6: 1617–24. - PubMed

Publication types

MeSH terms