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There are knowledge gaps concerning dynamics of extended-spectrum cephalosporin (ESC)-resistant  Escherichia coli  and their plasmids in broiler production and the persistence of strains on broiler farms. Thus, we aimed at characterising ESC-resistant  Escherichia coli  collected from all flocks reared on 10 different farms during a six-months sampling period. All isolates ( n  = 43) were subjected to whole-genome sequencing, and a subset of isolates ( n  = 7) were also sequenced using oxford nanopore technology and subsequent hybrid assembly in order to do in-depth characterisation of the ESC resistance plasmids. The 43 isolates belonged to 11 different sequence types, and three different ESC resistance gene/plasmid combinations were present, namely, IncK2/ bla  CMY-2  ( n  = 29), IncI1/ bla  CMY-2  ( n  = 6) and IncI1/ bla  CTX-M-1  ( n  = 8). ESC-resistant  E. coli  of different STs and with different ESC resistance gene/plasmid combinations could be present on the same farm, while a single ST and ESC resistance gene/plasmid displaying zero or few SNP differences were present on other farms. In-depth characterisation of IncK2/ bla  CMY-2  plasmids revealed that at least two distinct variants circulate in the broiler production. These plasmids showed close homology to previously published plasmids from other countries. Our longitudinal study show that ESC-resistant  E. coli  belong to a multitude of different STs and that different ESC resistance genes and plasmids occur. However, there is also indication of persistence of both ESC-resistant  E. coli  strains and IncK2/ bla  CMY-2  plasmids on farms. Further studies are warranted to determine the dynamics of strains, plasmids and ESC resistance genes within single broiler flocks.

frontiers in microbiology

Longitudinal Sampling Reveals Persistence of and Genetic Diversity in Extended-Spectrum Cephalosporin-Resistant Escherichia coli From Norwegian Broiler Production