Steady existence of Escherichia coli co-resistant to carbapenem and colistin in an animal breeding area even after the colistin forbidden

Carbapenem- and colistin-resistant Escherichia coli (CCREC) cause high mortality rates and health costs, and have become serious health concerns. Total 1764 samples were collected from 60 animal farms in 2019 and 2021, including worker and animal faeces, wastewater, well water, air, vegetables, human hands, object surfaces, throat swabs, soil, and flies to investigate the prevalence and potential transmission pathways of CCREC. Eleven CCREC were detected: 9 (5 in 2019 and 4 in 2021) from 5 worker faeces, 3 animal faeces, 1 wastewater, and 2 from 1 flies sample. Chicken farms had the highest number of CCREC (n = 9). The detection rate was low (<1.1%) overall, and there was no significant difference in both years, indicating that CCREC existed stably after 4 years of colistin ban. The combinations of chromosomes and plasmids harbouring bla NDM and mcr-1.1 were divided into 4 patterns: IncX3 plasmid -bla NDM & chromosome -mcr.1.1 (n = 5); IncX3 plasmid -bla NDM & IncHI2 plasmid -mcr.1.1 (n = 3); IncFII plasmid -bla NDM & IncI2 plasmid -mcr.1.1 (n = 2); both chromosome (n = 1). The bla NDM located on plasmids was surrounded by similar genetic structures: Tn3-IS-bla NDM -bleMBL-TrpF-DsbD-IS. The genetic contexts of mcr-1.1 were highly similar, with ‘ ISApl1-mcr-1.1-PAP2 ’ and ‘ mcr-1.1-PAP2 ’. All plasmids can be successfully transferred into E. coli J53, except for the IncHI2 plasmids with the transfer rate of 33.3%. The IncFII and IncI2 plasmids from same strain of flies could be co-transferred. The clonal spread of CCREC from humans to humans occurred on the same pig farm (P4) or different chicken farms (BC9 and LH7). This study suggested that flies, chromosomes, and plasmids jointly contribute to the steady existence of CCREC.