Antibiotic Resistance Gene Identification

The identification of putative determinants conferring resistance to quinolones, erythromycin, aminoglycosides and tetracycline was performed as previously described [35 (link)]. Briefly, assembled contigs were screened for AMR-associated genes with ABRicate (version 0.8.10; https://github.com/tseemann/abricate) using the National Center for Biotechnology Information (NCBI) database [36 (link)], ResFinder 3.0 [37 (link)] and the Comprehensive Antibiotic Resistance Database (CARD) v3.1.0 [38 (link)], with a threshold for the identification of acquired genes of 90 % identity and 60 % minimum length. Chromosomal resistance-mediating point mutations were identified using the PointFinder database embedded in ResFinder 4.0 [39 (link)].

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Ghielmetti G., Seth-Smith H.M., Roloff T., Cernela N., Biggel M., Stephan R, & Egli A. (2023). Whole-genome-based characterization of Campylobacter jejuni from human patients with gastroenteritis collected over an 18 year period reveals increasing prevalence of antimicrobial resistance. Microbial Genomics, 9(2), mgen000941.

Publication 2023

Aminoglycosides Antibiotic resistance Chromosomal Erythromycin Genes Point mutations Quinolones Tetracycline

Corresponding Organization :

Other organizations : University of Basel, University of Zurich, SIB Swiss Institute of Bioinformatics, University Hospital of Basel

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Variable analysis

independent variables

Assembled contigs

dependent variables

Identification of putative determinants conferring resistance to quinolones, erythromycin, aminoglycosides and tetracycline

control variables

Not explicitly mentioned

controls

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