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Increasing levels of antimicrobial resistance (AMR) have been documented in  Escherichia coli  causing travellers’ diarrhoea, particularly to the third-generation cephalosporins. Diarrhoeagenic  E. coli  (DEC) can act as a reservoir for the exchange of AMR genes between bacteria residing in the human gut, enabling them to survive and flourish through the selective pressures of antibiotic treatments. Using Oxford Nanopore Technology (ONT), we sequenced eight isolates of DEC from four patients’ specimens who had all recently returned to the United Kingdome from Pakistan. Sequencing yielded two DEC harbouring  bla  CTX-M-15  per patient, all with different sequence types (ST) and belonging to five different pathotypes. The study aimed to determine whether  bla  CTX-M-15  was located on the chromosome or plasmid and to characterise the drug-resistant regions to better understand the mechanisms of onward transmission of AMR determinants. Patients A and C both had one isolate where  bla  CTX-M-15  was located on the plasmid (899037 &amp;amp; 623213, respectively) and one chromosomally encoded (899091 &amp;amp; 623214, respectively). In patient B,  bla  CTX-M-15  was plasmid-encoded in both DEC isolates (786605 &amp;amp; 7883090), whereas in patient D,  bla  CTX-M-15  was located on the chromosome in both DEC isolates (542093 &amp;amp; 542099). The two  bla  CTX-M-15 -encoding plasmids associated with patient B were different although the  bla  CTX-M-15 -encoding plasmid isolated from 788309 (IncFIB) exhibited high nucleotide similarity to the  bla  CTX-M-15 -encoding plasmid isolated from 899037 (patient A). In the four isolates where  bla  CTX-M-15  was chromosomally encoded, two isolates (899091 &amp;amp; 542099) shared the same insertion site. The  bla  CTX-M-15  insertion site in isolate 623214 was described previously, whereas that of isolate 542093 was unique to this study. Analysis of Nanopore sequencing data enables us to characterise the genomic architecture of mobile genetic elements encoding AMR determinants. These data may contribute to a better understanding of persistence and onward transmission of AMR determinants in multidrug-resistant (MDR)  E. coli  causing gastrointestinal and extra-intestinal infections.

frontiers in microbiology

Use of Nanopore Sequencing to Characterise the Genomic Architecture of Mobile Genetic Elements Encoding blaCTX-M-15 in Escherichia coli Causing Travellers’ Diarrhoea