Longitudinal study on the genetic diversity of extended-spectrum cephalosporin resistant Escherichia coli in Dutch veal calves

The present study aimed to evaluate the genetic diversity of Extended Spectrum Cephalosporin resistant (ESC-R) <i>E. coli</i> isolates obtained from Dutch veal calves during a longitudinal study, to better understand the genetic background behind the persistent ESC-R <i>E. coli</i> colonization in the dairy and veal sectors. Rectal swabs were collected from 683 calves located in 13 Dutch dairy farms 1 day prior to their transportation to 8 veal farms. At the veal farms, rectal swabs were collected at 5 different time points after arrival. A total of 1,202 ESC-R <i>E. coli</i> isolates were obtained through selective isolation. Nine out of 13 dairy farms were positive for ESC-R <i>E. coli</i> (<i>n</i> = 175 isolates), arbitrarily divided in a high prevalence (>50%, <i>n</i> = 7) or low prevalence farms (<5%, <i>n</i> = 2) In three veal farms, a relatively high frequency of ESC-R <i>E. coli</i> was observed (range = 38-84%) while in the remaining five farms, a lower frequency was observed (range = 5-24%). At veal farms, the highest average ESC-R <i>E. coli</i> frequency was detected in week two (57.3%). ESBL/AmpC encoding genes were identified by RT-PCR and amplicon sequencing. ESBL genes (<i>bla</i> _CTX-M-1 groups, <i>bla</i> _CTX-M-9 group) and specific point mutations in the promotor region of the chromosomal <i>bla</i> _ampC gene were identified both at dairy farms and veal farms. A total of 364 ESC-R <i>E. coli</i> isolates were further characterized by WGS to determine the genetic relationship using core genome Multi Locus Sequencing Typing (cgMLST). The ESBL-genes <i>bla</i> _CTX-M-1 and <i>bla</i> _CTX-M-15 were predominant, the majority in combination with a non-ESBL <i>bla</i> _TEM-1 gene. In addition, genes encoding resistance against quinolones, aminoglycosides, phenicols, tetracyclines, sulfonamides, and trimethoprim were identified in these isolates. Finally, phylogenetic analysis showed a diverse pool of <i>E. coli</i> strains carrying the <i>bla</i> _CTX-M-1 gene, while two genetically closely related sequence types (STs) were identified in <i>E. coli</i> strains carrying the <i>bla</i> _CTX-M-15, being ST 4981 and ST 2325, the most predominant STs identified. Our results revealed a population of ESC-R <i>E. coli</i> which are genetically similar within veal farms and provides evidence of direct transmission and dissemination of ESC-R <i>E. coli</i> between the animals during the rearing process.