Characterization of Third-Generation Cephalosporin-Resistant <i>Escherichia coli</i> Isolated from Pigs in Cuba Using Next-Generation Sequencing

Abstract

Resistance to third-generation cephalosporins (3GC) in Escherichia coli has been reported worldwide from humans and animals, but the situation in Cuba is still poorly understood. This study aimed to gain new insights into the phenotypic and genotypic characteristics of third-generation cephalosporin-resistant (3GC-R) E. coli isolated from pigs in Cuba. Rectal swabs from 215 healthy pigs were taken from different municipalities in the western region of Cuba and spread on MacConkey agar supplemented with cefotaxime and ceftazidime. Ninety-six isolates were identified as 3GC-R E. coli and 87.5% of them were resistant to at least three antibiotic classes as determined by the measurement of the minimum inhibitory concentration (MIC) of 14 antibiotics. Twenty-seven different isolates were selected for Illumina next-generation sequencing, and subsequent in silico analysis was performed for the detection of antibiotic resistance and virulence genes, plasmid incompatibility (Inc) groups, multilocus sequence typing (MLST), and core genome MLST (cgMLST). The sequenced isolates contained extended-spectrum β-lactamase genes bla CTX-M-32 ( n = 17), bla CTX-M-15 ( n = 5), and bla CTX-M-55 ( n = 4) as well as with pAmpC gene bla CMY-2 ( n = 2). They also harbored genes for resistance to other clinically important classes of antibiotics, as well as several diverse virulence factors. The 3GC-R E. coli were genetically highly diverse, belonging to 16 different sequence types. IncX1 was the most frequent Inc group. The presence of 3GC-R E. coli in pigs from Cuba containing several different antibiotic resistance mechanisms emphasizes the need for surveillance programs and the establishment of strategies for the prudent use of antibiotics in food-producing animals.

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