A new multidrug‐resistant enterotoxigenic Escherichia coli pulsed‐field gel electrophoresis cluster associated with enrofloxacin non‐susceptibility in diseased pigs

Abstract

Aims To describe the temporal trends in Escherichia coli pathotypes and antimicrobial resistance detected in isolates from diseased‐pig cases submitted to the EcL from 2008 to 2016, in Quebec, Canada, and to investigate the presence of spatiotemporal and phylogenetic clusters. Methods and Results Detection of 12 genes coding for virulence factors in pathogenic E. coli in pigs by PCR and antimicrobial resistance standard disc diffusion assay were performed. Demographic and clinical data were entered in the Animal Pathogenic and Zoonotic E. coli (APZEC) database. ETEC:F4 was the most prevalent pathovirotype among the 3773 cases submitted. The LT:STb:F4 virotype was predominant until 2014, then was overtaken by the LT:STb:STa:F4 virotype. More than 90% of the ETEC:F4 isolates were multidrug resistant. A spatiotemporal cluster of LT:STb:STa:F4 isolates non‐susceptible to enrofloxacin was detected between 4/2015 and 9/2016. Pulsed‐field gel electrophoresis analysis of 137 ETEC:F4 isolates revealed the presence of a cluster composed mainly of LT:STb:STa:F4 isolates non‐susceptible to enrofloxacin. Conclusions The APZEC database was useful to highlight temporal trends in E. coli pathotypes. A high‐risk ETEC:F4 clone might disseminate in the pig population in Quebec since 2015. Significance and Impact of the Study Surveillance is crucial to identify new clones and develop control strategies.

High Risk Clone: A Proposal of Criteria Adapted to the One Health Context with Application to Enterotoxigenic Escherichia coli in the Pig Population

“…We demonstrated that the clone A-I appeared in 2013 and became predominant in 2015 (data from this study and [ 16 ]), consequently meeting the emergence criteria (cf Table 1 ). The clonality of ETEC isolates from various states of the USA and belonging to clonal lineage A had already been demonstrated [ 20 ].…”

“…Although our data demonstrate the capacity of WGS to refine the analysis for detecting clones, they also show that the combination of MLST and serotype data can accurately discriminate clonal lineages. On the other hand, when we compared these results to those obtained with PFGE in our previous study, we observed that only two thirds of the isolates analyzed with both methods were classified correctly by the PFGE when the cut-off of 55% of similarity was used to define a cluster [ 16 ]. Price et al found a similar misclassification for the E. coli ST131 [ 32 ].…”

“…An additional clone C1, comprising isolates belonging to ST772 and serogroup O23 and having a specific virotype STa:STb:F4 infrequently described in Quebec previously [ 16 ], was first observed in 2016. As all these isolates are MDR (non susceptible to tetracycline, TMS and one antimicrobial in the aminoglycoside category), they should be monitored during the coming years to evaluate if they could develop into a high risk clone and represent a threat for porcine health in Quebec and in North America.…”

“…In a preliminary study, ETEC:F4 isolates, coming from diseased (mostly diarrhea or sudden death) pigs were examined by PFGE as described previously [ 39 ]. These isolates were randomly selected from the Animal Pathogenic and Zoonotic E. coli (APZEC) database ( accessed on 28 February 2021) [ 16 ] as follows: 90 isolates from between 1990 and 2012, and 46 or 47 isolates per year from 2013 to 2016 inclusively. A phylogenetic tree based on the PFGE profiles of these 274 isolates was generated using the UPGMA method.…”

“…Pigs with diarrhea associated with ETEC have been commonly treated with ampicillin (alone or in combination with clavulanic acid), trimethoprim, sulfonamides, aminoglycosides (i.e., neomycin), ceftiofur, spectinomycin, or enrofloxacin, depending on the country [ 15 ]. In a previous article, we reported the presence of a cluster of ETEC:F4 isolates sharing at least 55% of similarity based on their pulse field gel electrophoresis (PFGE) profile in diseased pigs in Quebec, which emerged in 2013 [ 16 ]. Most of these isolates were LT:STb:STa:F4 and non-susceptible (intermediate or resistant) to enrofloxacin.…”