Use of Nanopore Sequencing to Characterise the Genomic Architecture of Mobile Genetic Elements Encoding blaCTX-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

Matthew T. Bird^*
, David R. Greig
, Satheesh Nair
, Claire Jenkins
, Gauri Godbole
, Saheer E. Gharbia

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

7 Citations (Scopus)

79 Downloads (Pure)

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.

Original language	English
Article number	862234
Journal	Frontiers in Microbiology
Volume	13
DOIs	https://doi.org/10.3389/fmicb.2022.862234
Publication status	Published - 29 Mar 2022

Bibliographical note

Funding Information: Health Protection Research Unit (HPRU) in Genomics and
Enabling Data is a collaboration funded by the National Institute for Health Research (NIHR) between UK Health Security Agency (UKHSA), the University of Warwick, the Centre for Genomic Pathogen Surveillance and the University of Cambridge. Health Protection Research Unit (HPRU) in Gastrointestinal Infections is a collaboration funded by the National Institute for Health Research (NIHR) at the University of Liverpool in partnership with UK Health Security Agency (UKHSA) and the University of Warwick.

Open Access: This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

Publisher Copyright: Copyright © 2022 Bird, Greig, Nair, Jenkins, Godbole and Gharbia.

Citation: Bird MT, Greig DR, Nair S, Jenkins C, Godbole G and Gharbia SE (2022) Use of Nanopore Sequencing to Characterise the Genomic Architecture of Mobile Genetic Elements Encoding blaCTX-M-15 in Escherichia coli Causing Travellers’ Diarrhoea. Front. Microbiol. 13:862234.

DOI: 10.3389/fmicb.2022.862234

Keywords

antibiotic resistance
bla
chromosomal integration
mobile genetic element
nanopore sequencing
plasmid

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This output contributes to the following UN Sustainable Development Goals (SDGs)

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Cite this

@article{4cad8ed118d54d6ca4095b16e4ec859c,

title = "Use of Nanopore Sequencing to Characterise the Genomic Architecture of Mobile Genetic Elements Encoding blaCTX-M-15 in Escherichia coli Causing Travellers{\textquoteright} Diarrhoea",

abstract = "Increasing levels of antimicrobial resistance (AMR) have been documented in Escherichia coli causing travellers{\textquoteright} 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{\textquoteright} specimens who had all recently returned to the United Kingdome from Pakistan. Sequencing yielded two DEC harbouring blaCTX-M-15 per patient, all with different sequence types (ST) and belonging to five different pathotypes. The study aimed to determine whether blaCTX-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 blaCTX-M-15 was located on the plasmid (899037 \& 623213, respectively) and one chromosomally encoded (899091 \& 623214, respectively). In patient B, blaCTX-M-15 was plasmid-encoded in both DEC isolates (786605 \& 7883090), whereas in patient D, blaCTX-M-15 was located on the chromosome in both DEC isolates (542093 \& 542099). The two blaCTX-M-15-encoding plasmids associated with patient B were different although the blaCTX-M-15-encoding plasmid isolated from 788309 (IncFIB) exhibited high nucleotide similarity to the blaCTX-M-15-encoding plasmid isolated from 899037 (patient A). In the four isolates where blaCTX-M-15 was chromosomally encoded, two isolates (899091 \& 542099) shared the same insertion site. The blaCTX-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, bla, chromosomal integration, mobile genetic element, nanopore sequencing, plasmid",

author = "Bird, \{Matthew T.\} and Greig, \{David R.\} and Satheesh Nair and Claire Jenkins and Gauri Godbole and Gharbia, \{Saheer E.\}",

note = "Funding Information: Health Protection Research Unit (HPRU) in Genomics and Enabling Data is a collaboration funded by the National Institute for Health Research (NIHR) between UK Health Security Agency (UKHSA), the University of Warwick, the Centre for Genomic Pathogen Surveillance and the University of Cambridge. Health Protection Research Unit (HPRU) in Gastrointestinal Infections is a collaboration funded by the National Institute for Health Research (NIHR) at the University of Liverpool in partnership with UK Health Security Agency (UKHSA) and the University of Warwick. Open Access: This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. Publisher Copyright: Copyright {\textcopyright} 2022 Bird, Greig, Nair, Jenkins, Godbole and Gharbia. Citation: Bird MT, Greig DR, Nair S, Jenkins C, Godbole G and Gharbia SE (2022) Use of Nanopore Sequencing to Characterise the Genomic Architecture of Mobile Genetic Elements Encoding blaCTX-M-15 in Escherichia coli Causing Travellers{\textquoteright} Diarrhoea. Front. Microbiol. 13:862234. DOI: 10.3389/fmicb.2022.862234",

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doi = "10.3389/fmicb.2022.862234",

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T1 - Use of Nanopore Sequencing to Characterise the Genomic Architecture of Mobile Genetic Elements Encoding blaCTX-M-15 in Escherichia coli Causing Travellers’ Diarrhoea

AU - Bird, Matthew T.

AU - Greig, David R.

AU - Nair, Satheesh

AU - Jenkins, Claire

AU - Godbole, Gauri

AU - Gharbia, Saheer E.

N1 - Funding Information: Health Protection Research Unit (HPRU) in Genomics and Enabling Data is a collaboration funded by the National Institute for Health Research (NIHR) between UK Health Security Agency (UKHSA), the University of Warwick, the Centre for Genomic Pathogen Surveillance and the University of Cambridge. Health Protection Research Unit (HPRU) in Gastrointestinal Infections is a collaboration funded by the National Institute for Health Research (NIHR) at the University of Liverpool in partnership with UK Health Security Agency (UKHSA) and the University of Warwick. Open Access: This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. Publisher Copyright: Copyright © 2022 Bird, Greig, Nair, Jenkins, Godbole and Gharbia. Citation: Bird MT, Greig DR, Nair S, Jenkins C, Godbole G and Gharbia SE (2022) Use of Nanopore Sequencing to Characterise the Genomic Architecture of Mobile Genetic Elements Encoding blaCTX-M-15 in Escherichia coli Causing Travellers’ Diarrhoea. Front. Microbiol. 13:862234. DOI: 10.3389/fmicb.2022.862234

PY - 2022/3/29

Y1 - 2022/3/29

N2 - 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 blaCTX-M-15 per patient, all with different sequence types (ST) and belonging to five different pathotypes. The study aimed to determine whether blaCTX-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 blaCTX-M-15 was located on the plasmid (899037 & 623213, respectively) and one chromosomally encoded (899091 & 623214, respectively). In patient B, blaCTX-M-15 was plasmid-encoded in both DEC isolates (786605 & 7883090), whereas in patient D, blaCTX-M-15 was located on the chromosome in both DEC isolates (542093 & 542099). The two blaCTX-M-15-encoding plasmids associated with patient B were different although the blaCTX-M-15-encoding plasmid isolated from 788309 (IncFIB) exhibited high nucleotide similarity to the blaCTX-M-15-encoding plasmid isolated from 899037 (patient A). In the four isolates where blaCTX-M-15 was chromosomally encoded, two isolates (899091 & 542099) shared the same insertion site. The blaCTX-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.

AB - 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 blaCTX-M-15 per patient, all with different sequence types (ST) and belonging to five different pathotypes. The study aimed to determine whether blaCTX-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 blaCTX-M-15 was located on the plasmid (899037 & 623213, respectively) and one chromosomally encoded (899091 & 623214, respectively). In patient B, blaCTX-M-15 was plasmid-encoded in both DEC isolates (786605 & 7883090), whereas in patient D, blaCTX-M-15 was located on the chromosome in both DEC isolates (542093 & 542099). The two blaCTX-M-15-encoding plasmids associated with patient B were different although the blaCTX-M-15-encoding plasmid isolated from 788309 (IncFIB) exhibited high nucleotide similarity to the blaCTX-M-15-encoding plasmid isolated from 899037 (patient A). In the four isolates where blaCTX-M-15 was chromosomally encoded, two isolates (899091 & 542099) shared the same insertion site. The blaCTX-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.

KW - antibiotic resistance

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KW - chromosomal integration

KW - mobile genetic element

KW - nanopore sequencing

KW - plasmid

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