Genetic Features of mcr-1 Mediated Colistin Resistance in CMY-2-Producing Escherichia coli From Romanian Poultry

Abstract

Colistin is a last resort antibiotic used for the treatment of human infections associated with carbapenemase-producing Enterobacteriales. Here, we evaluated the occurrence of <i>mcr-1</i> and <i>-2</i> plasmid-mediated colistin resistance in colistin and/or carbapenem resistant human clinical Enterobacteriales and other gram-negative bacteria (<i>n</i> = 543) as well as third generation cephalosporin-resistant (3GCR) <i>Escherichia coli</i> isolates from poultry abattoir workers (<i>n</i> = 15) and poultry fecal samples (<i>n</i> = 92) collected from two geographically separate abattoirs in Romania. which revealed that <i>mcr-1</i> was present within four sequence types (STs): ST744 (<i>n</i> = 7), ST57 (<i>n</i> = 7), ST156 (<i>n</i> = 2), and ST10 (<i>n</i> = 1). Within STs, serotypes were conserved and, notably, all except one of the <i>mcr-1-</i>positive isolates were found to exhibit fluoroquinolone-resistance (FQR) associated SNPs in both <i>gyrA</i> and <i>parC</i>. While there were variations in genotypes, all isolates belonging to ST744, ST57, and ST156 were rich in resistance determinants, carrying aminoglycoside-modifying enzymes genes, sulfonamide resistance gene <i>bla</i> _TEM- ₁ as well as <i>bla</i> _CMY- ₂ AmpC β-lactamase resistance genes. They also exhibited high similarity in carriage of virulence genes; ST10, however, only carried the <i>mcr-1</i> gene. Whole genome sequencing (WGS) analysis also revealed that although the <i>mcr-1</i> gene was identified in a diverse population of <i>E. coli</i>, two STs (ST57 and ST744) predominated and interestingly, were found in isolates across both abattoirs providing evidence for clonal transmission. Also, two main genomic contexts of <i>mcr-1</i> isolates were revealed with all ST57 isolates harboring the <i>mcr-1</i> gene between two copies of IS<i>Apl1</i> (or the Tn<i>6330</i> transposon) whilst a common <i>mcr-1</i> containing scaffold, highly similar to IncX type <i>mcr-1</i>-bearing plasmids (pWI2-mcr, Accession number: LT838201), was present among <i>mcr-1</i> isolates of varying phylogenetic backgrounds (ST10, ST744 and ST156). The high prevalence of the <i>mcr-1</i> gene in poultry <i>E. coli</i> isolates with co-resistance to cephalosporins and quinolones, in a country where antimicrobial use in food production species is poorly regulated, is concerning and the findings from this study should lead to better surveillance of antimicrobial resistance (AMR) in food-production animals in Romania.