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Whole-Genome Sequencing-Based Antimicrobial Resistance Characterization and Phylogenomic Investigation of 19 Multidrug-Resistant and Extended-Spectrum Beta-Lactamase-Positive Escherichia coli Strains Collected From Hospital Patients in Benin in 2019

The increasing worldwide prevalence of extended-spectrum beta-lactamase (ESBL) producing Escherichia coli constitutes a serious threat to global public health. Surgical site infections are associated with high morbidity and mortality rates in developing countries, fueled by the limited availability...

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Autores principales: Yehouenou, Carine Laurence, Bogaerts, Bert, De Keersmaecker, Sigrid C. J., Roosens, Nancy H. C., Marchal, Kathleen, Tchiakpe, Edmond, Affolabi, Dissou, Simon, Anne, Dossou, Francis Moise, Vanneste, Kevin, Dalleur, Olivia
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8695880/
https://www.ncbi.nlm.nih.gov/pubmed/34956117
http://dx.doi.org/10.3389/fmicb.2021.752883
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author Yehouenou, Carine Laurence
Bogaerts, Bert
De Keersmaecker, Sigrid C. J.
Roosens, Nancy H. C.
Marchal, Kathleen
Tchiakpe, Edmond
Affolabi, Dissou
Simon, Anne
Dossou, Francis Moise
Vanneste, Kevin
Dalleur, Olivia
author_facet Yehouenou, Carine Laurence
Bogaerts, Bert
De Keersmaecker, Sigrid C. J.
Roosens, Nancy H. C.
Marchal, Kathleen
Tchiakpe, Edmond
Affolabi, Dissou
Simon, Anne
Dossou, Francis Moise
Vanneste, Kevin
Dalleur, Olivia
author_sort Yehouenou, Carine Laurence
collection PubMed
description The increasing worldwide prevalence of extended-spectrum beta-lactamase (ESBL) producing Escherichia coli constitutes a serious threat to global public health. Surgical site infections are associated with high morbidity and mortality rates in developing countries, fueled by the limited availability of effective antibiotics. We used whole-genome sequencing (WGS) to evaluate antimicrobial resistance and the phylogenomic relationships of 19 ESBL-positive E. coli isolates collected from surgical site infections in patients across public hospitals in Benin in 2019. Isolates were identified by MALDI-TOF mass spectrometry and phenotypically tested for susceptibility to 16 antibiotics. Core-genome multi-locus sequence typing and single-nucleotide polymorphism-based phylogenomic methods were used to investigate the relatedness between samples. The broader phylogenetic context was characterized through the inclusion of publicly available genome data. Among the 19 isolates, 13 different sequence types (STs) were observed, including ST131 (n = 2), ST38 (n = 2), ST410 (n = 2), ST405 (n = 2), ST617 (n = 2), and ST1193 (n = 2). The bla(CTX-M-15) gene encoding ESBL resistance was found in 15 isolates (78.9%), as well as other genes associated with ESBL, such as bla(OXA-1) (n = 14) and bla(TEM-1) (n = 9). Additionally, we frequently observed genes encoding resistance against aminoglycosides [aac-(6')-Ib-cr, n = 14], quinolones (qnrS(1), n = 4), tetracyclines [tet(B), n = 14], sulfonamides (sul2, n = 14), and trimethoprim (dfrA17, n = 13). Nonsynonymous chromosomal mutations in the housekeeping genes parC and gyrA associated with resistance to fluoroquinolones were also detected in multiple isolates. Although the phylogenomic investigation did not reveal evidence of hospital-acquired transmissions, we observed two very similar strains collected from patients in different hospitals. By characterizing a set of multidrug-resistant isolates collected from a largely unexplored environment, this study highlights the added value for WGS as an effective early warning system for emerging pathogens and antimicrobial resistance.
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spelling pubmed-86958802021-12-24 Whole-Genome Sequencing-Based Antimicrobial Resistance Characterization and Phylogenomic Investigation of 19 Multidrug-Resistant and Extended-Spectrum Beta-Lactamase-Positive Escherichia coli Strains Collected From Hospital Patients in Benin in 2019 Yehouenou, Carine Laurence Bogaerts, Bert De Keersmaecker, Sigrid C. J. Roosens, Nancy H. C. Marchal, Kathleen Tchiakpe, Edmond Affolabi, Dissou Simon, Anne Dossou, Francis Moise Vanneste, Kevin Dalleur, Olivia Front Microbiol Microbiology The increasing worldwide prevalence of extended-spectrum beta-lactamase (ESBL) producing Escherichia coli constitutes a serious threat to global public health. Surgical site infections are associated with high morbidity and mortality rates in developing countries, fueled by the limited availability of effective antibiotics. We used whole-genome sequencing (WGS) to evaluate antimicrobial resistance and the phylogenomic relationships of 19 ESBL-positive E. coli isolates collected from surgical site infections in patients across public hospitals in Benin in 2019. Isolates were identified by MALDI-TOF mass spectrometry and phenotypically tested for susceptibility to 16 antibiotics. Core-genome multi-locus sequence typing and single-nucleotide polymorphism-based phylogenomic methods were used to investigate the relatedness between samples. The broader phylogenetic context was characterized through the inclusion of publicly available genome data. Among the 19 isolates, 13 different sequence types (STs) were observed, including ST131 (n = 2), ST38 (n = 2), ST410 (n = 2), ST405 (n = 2), ST617 (n = 2), and ST1193 (n = 2). The bla(CTX-M-15) gene encoding ESBL resistance was found in 15 isolates (78.9%), as well as other genes associated with ESBL, such as bla(OXA-1) (n = 14) and bla(TEM-1) (n = 9). Additionally, we frequently observed genes encoding resistance against aminoglycosides [aac-(6')-Ib-cr, n = 14], quinolones (qnrS(1), n = 4), tetracyclines [tet(B), n = 14], sulfonamides (sul2, n = 14), and trimethoprim (dfrA17, n = 13). Nonsynonymous chromosomal mutations in the housekeeping genes parC and gyrA associated with resistance to fluoroquinolones were also detected in multiple isolates. Although the phylogenomic investigation did not reveal evidence of hospital-acquired transmissions, we observed two very similar strains collected from patients in different hospitals. By characterizing a set of multidrug-resistant isolates collected from a largely unexplored environment, this study highlights the added value for WGS as an effective early warning system for emerging pathogens and antimicrobial resistance. Frontiers Media S.A. 2021-12-09 /pmc/articles/PMC8695880/ /pubmed/34956117 http://dx.doi.org/10.3389/fmicb.2021.752883 Text en Copyright © 2021 Yehouenou, Bogaerts, De Keersmaecker, Roosens, Marchal, Tchiakpe, Affolabi, Simon, Dossou, Vanneste and Dalleur. https://creativecommons.org/licenses/by/4.0/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.
spellingShingle Microbiology
Yehouenou, Carine Laurence
Bogaerts, Bert
De Keersmaecker, Sigrid C. J.
Roosens, Nancy H. C.
Marchal, Kathleen
Tchiakpe, Edmond
Affolabi, Dissou
Simon, Anne
Dossou, Francis Moise
Vanneste, Kevin
Dalleur, Olivia
Whole-Genome Sequencing-Based Antimicrobial Resistance Characterization and Phylogenomic Investigation of 19 Multidrug-Resistant and Extended-Spectrum Beta-Lactamase-Positive Escherichia coli Strains Collected From Hospital Patients in Benin in 2019
title Whole-Genome Sequencing-Based Antimicrobial Resistance Characterization and Phylogenomic Investigation of 19 Multidrug-Resistant and Extended-Spectrum Beta-Lactamase-Positive Escherichia coli Strains Collected From Hospital Patients in Benin in 2019
title_full Whole-Genome Sequencing-Based Antimicrobial Resistance Characterization and Phylogenomic Investigation of 19 Multidrug-Resistant and Extended-Spectrum Beta-Lactamase-Positive Escherichia coli Strains Collected From Hospital Patients in Benin in 2019
title_fullStr Whole-Genome Sequencing-Based Antimicrobial Resistance Characterization and Phylogenomic Investigation of 19 Multidrug-Resistant and Extended-Spectrum Beta-Lactamase-Positive Escherichia coli Strains Collected From Hospital Patients in Benin in 2019
title_full_unstemmed Whole-Genome Sequencing-Based Antimicrobial Resistance Characterization and Phylogenomic Investigation of 19 Multidrug-Resistant and Extended-Spectrum Beta-Lactamase-Positive Escherichia coli Strains Collected From Hospital Patients in Benin in 2019
title_short Whole-Genome Sequencing-Based Antimicrobial Resistance Characterization and Phylogenomic Investigation of 19 Multidrug-Resistant and Extended-Spectrum Beta-Lactamase-Positive Escherichia coli Strains Collected From Hospital Patients in Benin in 2019
title_sort whole-genome sequencing-based antimicrobial resistance characterization and phylogenomic investigation of 19 multidrug-resistant and extended-spectrum beta-lactamase-positive escherichia coli strains collected from hospital patients in benin in 2019
topic Microbiology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8695880/
https://www.ncbi.nlm.nih.gov/pubmed/34956117
http://dx.doi.org/10.3389/fmicb.2021.752883
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