Within-host heterogeneity and flexibility of mcr-1 transmission in chicken gut.

• A single chicken could harbour up to three different bacterial species carrying the mcr-1 gene. • Whole-genome sequencing revealed high heterogeneity of mcr-1 -positive Escherichia coli isolates within a single host. • Within the same chicken, the mcr-1 gene could be carried by plasmids belonging to five different Inc types. • Great diversity was also observed in the eight IncI2 plasmids bearing the mcr-1 gene within a single chicken. • A novel IS Apl1 -mediated complex transposition was identified in E. coli. To characterize the colistin-resistant bacterial population in the gut and assess diversity of mcr-1 transmission within a single individual. Large numbers of isolates (>100 colonies/chicken cecum sample) were collected from nine randomly selected mcr-1 -positive chickens in China and used for comprehensive microbiological, molecular and comparative genomics analyses. Of 1273 colonies, 968 were mcr-1 positive (962 Escherichia coli , two Escherichia fergusonii , two Klebsiella pneumoniae and two Klebsiella quasipneumoniae). One to six colistin-resistant species and three to 10 E. coli pulsed-field gel electrophoresis (PFGE) clusters could be identified from each sample. Whole-genome sequencing (WGS) analysis of the representative E. coli strains revealed three to nine sequence types observed in a single chicken host. The mcr-1 genes are located in either chromosomes or plasmids of different types, including IncI2 (n =30), IncHI2 (n =14), IncX4 (n =4), p0111(n =2) and IncHI1(n =1). Strikingly, in single cecum samples, one to five Inc type plasmids harbouring mcr-1 could be identified. Great diversity was also observed for the same IncI2 plasmid within a single chicken host. In addition, up to eight genetic contexts of the mcr-1 gene occurred within a single chicken. There is extensive heterogeneity and flexibility of mcr-1 transmission in chicken gut due to bacterial species differences, distant clonal relatedness of isolates, many types and variations of mcr -positive plasmids, and the flexible genetic context of the mcr - 1 gene. These compelling findings indicate that the gut is a 'melting pot' for active horizontal transfer of the mcr-1 gene. [ABSTRACT FROM AUTHOR]