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Horizontal transfer of antibiotic resistance determinants contributes to dissemination of antibiotic resistance. Such transfer of resistance genes within the human gut has been documented in some  in vivo  studies. The present study investigated seven  bla   CTX-M-1 -carrying  Escherichia coli  isolates from three consecutive faecal samples collected from one cystic fibrosis patient in a nine-months period, by analysing whole genome sequencing data. The analyses showed that the seven  E .  coli  isolates represented three genetically diverse strains. All isolates contained  bla   CTX-M-1 -carrying Incl1 plasmids that shared a common 101 kb backbone differing by only four SNPs. The plasmids harboured by the three different  E .  coli  strains varied within limited regions suggestive of recombination events, according to the phylogenetic topology of the genomes of the isolates harbouring them. The findings strongly suggest that horizontal transfer of a  bla   CTX-M-1 -carrying plasmid had occurred within the patient´s gut. The study illustrates the within-host diversity of faecally carried resistant  E .  coli  isolates and highlights the value of collecting multiple bacterial colonies from longitudinally collected samples to assess faecal carriage of resistant enterobacteria. The clustering of the plasmids with the corresponding  E .  coli  strains carrying them indicates that the plasmids appear to have adapted to their respective  E .  coli  hosts.

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Transfer of a bla CTX-M-1-carrying plasmid between different Escherichia coli strains within the human gut explored by whole genome sequencing analyses