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

Matthew T Bird; David R Greig; Satheesh Nair; Claire Jenkins; Gauri Godbole; Saheer E Gharbia

doi:10.3389/fmicb.2022.862234

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

Front Microbiol. 2022 Mar 29:13:862234. doi: 10.3389/fmicb.2022.862234. eCollection 2022.

Authors

Matthew T Bird^{1

2}, David R Greig^{1

3

4}, Satheesh Nair¹, Claire Jenkins^{1

3}, Gauri Godbole¹, Saheer E Gharbia^{1

2}

Affiliations

¹ National Infection Service, UK Health Security Agency, London, United Kingdom.
² Health Protection Research Unit in Genomes and Enabling Data, Warwick, United Kingdom.
³ NIRH Health Protection Research Unit for Gastrointestinal Pathogens, Liverpool, United Kingdom.
⁴ Division of Infection and Immunity, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom.

Abstract

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 & 623213, respectively) and one chromosomally encoded (899091 & 623214, respectively). In patient B, bla _CTX-M-15 was plasmid-encoded in both DEC isolates (786605 & 7883090), whereas in patient D, bla _CTX-M-15 was located on the chromosome in both DEC isolates (542093 & 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 & 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.

Keywords: antibiotic resistance; blaCTX-M-15; chromosomal integration; mobile genetic element; nanopore sequencing; plasmid.