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Resistance Gene Screening and Integron Typing

CE Christa Ewers
AJ Anno de Jong
EP Ellen Prenger-Berninghoff
FG Farid El Garch
UL Ursula Leidner
ST Sumeet K. Tiwari
TS Torsten Semmler
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The web-based tool ResFinder 3.21, hosted at the Center for Genomic Epidemiology (CGE), was used to identify resistance genes and chromosomal mutations related to β-lactam (ampC promoter mutation), fluoroquinolone (mutations in gyrA, gyrB, parA, and parC), and colistin resistance (pmrAB) based on WGS (Zankari et al., 2012). Resistance gene screening was carried out by BLASTn (90% identity and 90% query coverage) analysis against homologous genes present in the Comprehensive Antibiotic Resistance Database2.

To investigate the distribution of class 1, class 2, and class 3 integrons with prevalent arrays in the genomes of our Escherichia spp. isolates, we performed BLAST search against the available databases GenBank and INTEGRALL 1.2, using filter parameters of more than 90% nucleotide identity and at least 80% query coverage.

Copyright and License information:  ©2021 Ewers, de Jong, Prenger-Berninghoff, El Garch, Leidner, Tiwari and Semmler.
This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

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