Molecular Characterization of Extended-Spectrum β-Lactamase-Producing Multidrug Resistant Escherichia coli From Swine in Northwest China

Abstract

<b>Objectives:</b> The aim of the present study was to explore the prevalence and molecular characterization of extended-spectrum β-lactamase (ESBL)-producing <i>Escherichia coli</i> collected from pig farms in Northwest China. <b>Methods:</b> Between May 2015 and June 2017, a total of 456 <i>E. coli</i> isolates were collected from fecal samples of healthy and diarrheal pigs in Northwest China to screen the ESBL producers. The β-lactamases, plasmid-mediated quinolone resistance (PMQR) genes and virulence genes among ESBL producers were corroborated by PCR and sequencing. Finally, ESBL producers were further grouped according to phylogenetic background and genetic relatedness. <b>Results:</b> Forty-four (9.6%) out of the 456 <i>E. coli</i> isolates were identified as ESBL-producing isolates. All ESBL producers exhibited multidrug resistance (MDR) phenotype, and more than 90% of the ESBL producers were resistant to amoxicillin, amoxicillin-clavulanic acid, oxytetracycline, enrofloxacin and sulfamethoxazole/trimethoprim. All ESBL producers harbored at least one type of β-lactamase, with <i>bla</i>_CTX-M, <i>bla</i>_TEM, <i>bla</i>_SHV, <i>bla</i>_OXA-48, and <i>bla</i>_KPC-2 being detected in forty, thirty, seven, four, two and one isolates, respectively. Sequencing revealed the most common <i>bla</i>_CTX-M subtype was <i>bla</i>_CTX-M-14 (<i>n</i> = 24), followed by <i>bla</i>_CTX-M-15 (<i>n</i> = 14), <i>bla</i>_CTX-M-64 (<i>n</i> = 11), <i>bla</i>_CTX-M-9 (<i>n</i> = 10) and <i>bla</i>_CTX-M-123 (<i>n</i> = 9). <i>qnrS</i> (<i>n</i> = 23) was the predominant PMQR gene, and all PMQR genes were detected in co-existence with β-lactamase genes. <i>estA</i> (<i>n</i> = 18) and F4 (<i>n</i> = 18) were the most prevalent enterotoxin and fimbrial adhesin, respectively, and 27 different virotypes were found with respect to the association of enterotoxins and fimbrial adhesins. Twenty-four different sequence types (STs) were identified among 44 ESBL producers, and clones ST405, ST10 and ST648 were strongly present in more than one-third (34.1%) of ESBL producers. <b>Conclusion:</b> All ESBL-producing <i>E. coli</i> isolates exhibited MDR phenotype, and showed high prevalence of β-lactamase and PMQR genes. Especially, one isolate harbored ESBL genes <i>bla</i>_TEM, <i>bla</i>_SHV, <i>bla</i>_CTX-M-9, <i>bla</i>_CTX-M-14, <i>bla</i>_CTX-M-64, and carbapenemase gene <i>bla</i>_OXA-48 and <i>bla</i>_KPC-2, as well as PMQR genes <i>qnrS, qnrB, qnrD, qepA</i> and <i>aac(6')-Ib-cr</i>.