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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使用下一代测序鉴定从古巴猪中分离的第三代头孢菌素抗性大肠杆菌

世界范围内已有人类和动物对大肠杆菌对第三代头孢菌素 (3GC) 产生耐药性的报道，但古巴的情况仍知之甚少。本研究旨在获得对从古巴猪中分离的第三代头孢菌素抗性 (3GC-R)大肠杆菌的表型和基因型特征的新见解。取自古巴西部地区不同城市的 215 头健康猪的直肠拭子，并在添加了头孢噻肟和头孢他啶的 MacConkey 琼脂上涂抹。96 株分离株被鉴定为 3GC-R大肠杆菌通过测量 14 种抗生素的最低抑菌浓度 (MIC) 确定，其中 87.5% 对至少三种抗生素类别具有抗性。选择了 27 个不同的分离株进行下一代 Illumina 测序，随后进行了计算机分析以检测抗生素耐药性和毒力基因、质粒不相容性 (Inc) 组、多位点序列分型 (MLST) 和核心基因组 MLST。 cgMLST）。测序的分离株含有超广谱 β-内酰胺酶基因bla _CTX-M-32 ( n  = 17)、bla _CTX-M-15 ( n  = 5) 和bla _CTX-M-55 ( n = 4) 以及 pAmpC 基因bla _CMY-2 ( n  = 2)。它们还含有对其他临床上重要的抗生素类别以及几种不同的毒力因子具有抗性的基因。3GC-R大肠杆菌在遗传上高度多样化，属于 16 种不同的序列类型。IncX1 是最常见的 Inc 组。来自古巴的猪中存在 3GC-R大肠杆菌，其中包含几种不同的抗生素抗性机制，需要进行监测计划并制定在食用动物中谨慎使用抗生素的策略。