Plasmid-Mediated Colistin Resistance (mcr-1) in Escherichia coli from Non-Imported Fresh Vegetables for Human Consumption in Portugal

Abstract

In this study, we report the presence of the plasmid-mediated colistin resistance (PMCR)-encoding gene <i>mcr-1</i> in an <i>Escherichia</i> <i>coli</i> isolate, INSali25, recovered from lettuce produced and marketed in Portugal. Colistin MIC from the vegetable <i>E. coli</i> isolate-determined by microdilution broth method according to EUCAST guidelines-revealed a non-wild-type phenotype of colistin (MIC 16 mg/L). To understand the genetic background of <i>E. coli</i> INSali25, we performed whole genome sequencing. Plasmid sequencing was also performed after plasmid DNA extraction from the transconjugant TcINSali25 (<i>mcr-1</i>). Directed bioinformatics analysis identified the <i>mcr-1</i> gene in a 39,998 bp length contig, with an upstream region including the antibiotic resistance gene <i>bla</i>_TEM-1 in a partial transposon Tn<i>2,</i> truncated by the insertion sequence IS<i>26</i> and showing >99% identity with previously described <i>mcr-1</i>-harboring IncHI2 plasmids. Further <i>in silico</i> analysis showed the presence of additional genes conferring resistance to β-lactams (<i>bla</i>_TEM-1), aminoglycosides (<i>aadA1</i>, <i>aph(4)-Ia</i>, <i>aph(6)-Id</i>, <i>aac(3)-Iv</i>), macrolides (<i>mdf(A)-</i>type), phenicol (<i>floR-</i>type), tetracycline (<i>tetA</i>), and sulphonamides (<i>sul2</i>). INSali25 isolate belonged to the ST1716 lineage and showed the <i>fimH54</i> and <i>fumC27</i> alleles. Lettuce is a vegetable that is commonly consumed fresh and not subjected to any cooking process, which may amplify human food safety risks. Moreover, the occurrence of plasmid-mediated colistin resistance in a sample that was not imported and was acquired in a large retail store reinforces the widespread distribution of <i>mcr-1</i>.