Occurrence of Mobile Colistin Resistance Genes <i>mcr-1</i>–<i>mcr-10</i> including Novel <i>mcr</i> Gene Variants in Different Pathotypes of Porcine <i>Escherichia coli</i> Isolates Collected in Germany from 2000 to 2021
2023
Lisa Göpel | Ellen Prenger-Berninghoff | Silver A. Wolf | Torsten Semmler | Rolf Bauerfeind | Christa Ewers
In the European Union, gastrointestinal disease in pigs is the main indication for the use of colistin, but large-scale epidemiologic data concerning the frequency of mobile colistin resistance (<i>mcr</i>) genes in pig-associated pathotypes of <i>Escherichia coli</i> (<i>E. coli</i>) are lacking. Multiplex polymerase chain reactions were used to detect virulence-associated genes (VAGs) and <i>mcr-1</i>–<i>mcr-10</i> genes in 10,573 porcine <i>E. coli</i> isolates collected in Germany from July 2000 to December 2021. Whole genome sequencing was performed on 220 representative <i>mcr</i>-positive <i>E. coli</i> strains. The total frequency of <i>mcr</i> genes was 10.2%, the most frequent being <i>mcr-1</i> (8.4%) and <i>mcr-4</i> (1.6%). All other <i>mcr</i> genes were rarely identified (<i>mcr-2</i>, <i>mcr-3</i>, <i>mcr-5</i>) or absent (<i>mcr-6</i> to <i>mcr-10</i>). The highest frequencies of <i>mcr</i> genes were found in enterotoxigenic and shiga toxin-encoding <i>E. coli</i> (ETEC/STEC hybrid) and in edema disease <i>E. coli</i> (EDEC) strains (21.9% and 17.7%, respectively). We report three novel <i>mcr</i> variants, <i>mcr-1.36</i>, <i>mcr-4.8</i>, and <i>mcr-5.5</i>. In 39 attaching and effacing <i>E. coli</i> (AEEC) isolates analyzed in our study, the <i>eae</i> subtype β1 was the most prevalent (71.8%). Constant surveillance for the presence of <i>mcr</i> genes in various sectors should consider the different frequency of <i>mcr</i>-positive isolates in pathogenic <i>E. coli</i>.
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