Prevalence of Cefotaxime-Resistant Escherichia coli Isolates from Healthy Cattle and Sheep in Northern Spain: Phenotypic and Genome-Based Characterization of Antimicrobial Susceptibility

• Published in: Applied and environmental microbiology Vol. 86; no. 15
• Main Authors: Tello, Maitane, Ocejo, Medelin, Oporto, Beatriz, Hurtado, Ana
• Format: Journal Article
• Language: English
• Published: United States American Society for Microbiology 20-07-2020
• Subjects: Animals; Anti-Bacterial Agents - pharmacology; Antimicrobial agents; Antimicrobial resistance; Carbapenemase; Cattle; Cattle Diseases - epidemiology; Cattle Diseases - microbiology; Cefotaxime; Cefotaxime - pharmacology; Cephalosporins; Ciprofloxacin; Colistin; Cross-Sectional Studies; Dairy cattle; Drug resistance; Drug Resistance, Bacterial; E coli; Epidemiology; Escherichia coli; Escherichia coli - drug effects; Escherichia coli - genetics; Escherichia coli - isolation & purification; Escherichia coli Infections - epidemiology; Escherichia coli Infections - microbiology; Escherichia coli Infections - veterinary; Genes; Genomes; Genotype; Imipenem; Meropenem; Microbial Sensitivity Tests - veterinary; Mutation; Phenotype; Phenotypes; Plasmids; Point mutation; Prevalence; Public and Environmental Health Microbiology; Sheep; Sheep Diseases - epidemiology; Sheep Diseases - microbiology; Spain - epidemiology; Sulfamethoxazole; Tigecycline; Trimethoprim; Spain; AmpC; WGS; AMR; MIC; whole-genome sequencing; AmpC β-lactamase-producing E. coli; minimum inhibitory concentration; beef cattle; dairy cattle; antimicrobial resistance; ESBL; extended-spectrum β-lactamase-producing E. coli; sheep
• ISSN: 0099-2240; 1098-5336
• DOI: 10.1128/AEM.00742-20

In order to estimate herd-level prevalence of extended-spectrum β-lactamase/AmpC β-lactamase (ESBL/AmpC)- and carbapenemase-producing commensal
in ruminants in the Basque Country (northern Spain), a cross-sectional survey was conducted in 2014 to 2016 in 300 herds using selective isolation. ESBL-/AmpC-producing
was isolated in 32.9% of dairy cattle herds, 9.6% of beef cattle herds, and 7.0% of sheep flocks. No carbapenemase-producing
was isolated. Phenotypic antimicrobial susceptibility determined by broth microdilution using EUCAST epidemiological cutoff values identified widespread coresistance to extended-spectrum cephalosporins and other antimicrobials (110/135 isolates), particularly tetracycline, sulfamethoxazole, trimethoprim, and ciprofloxacin. All isolates were susceptible to tigecycline, imipenem, meropenem, and colistin. The genomes of 66 isolates were sequenced using an Illumina NovaSeq 6000 and screened for antimicrobial resistance determinants against ResFinder and PointFinder. The plasmid/chromosomal locations of resistance genes were predicted with PlasFlow, and plasmid replicons were identified using PlasmidFinder. Fifty-two acquired resistance genes and point mutations in another four genes that coded for resistance to 11 antimicrobial classes were identified. Fifty-five genomes carried ESBL-encoding genes,
being the most common, and 11 carried determinants of the AmpC phenotype, mostly the
gene. Additionally, genes coding for β-lactamases of the CTX-M group 9 were detected as well as the sporadic presence of
,
, and a point mutation in the
promoter. Only a bovine isolate coharbored more than one ESBL/AmpC genetic determinant (
and a mutation in the
promoter), confirming its ESBL- and AmpC β-lactamase-producing phenotype. Most ESBL/AmpC genes were located in IncI1 plasmids, which also carried a great variety of other antimicrobial resistance genes.
Extended-spectrum β-lactamase (ESBL)- and AmpC β-lactamase (AmpC)-producing
isolates have emerged in recent years as some of the fastest spreading antimicrobial resistance determinants in humans and food-producing animals, becoming a concern for animal and public health. This study provided insight into the prevalence of cefotaxime-resistant
in cattle and sheep in the Basque Country and the associated genetic determinants of antimicrobial resistance. These constituted an important contribution to the limited repository of such data for cattle in the region and for sheep worldwide. Antimicrobial susceptibility testing by phenotypic and molecular methods is key in surveillance programs to enhance early detection of resistance development, monitor resistance trends, and provide guidance to clinicians in selecting the adequate therapy.