Comparative Genomic Analysis of Globally Dominant ST131 Clone with Other Epidemiologically Successful Extraintestinal Pathogenic <italic toggle="yes">Escherichia coli</italic> (ExPEC) Lineages

ABSTRACT Escherichia coli sequence type 131 (ST131), a pandemic clone responsible for the high incidence of extraintestinal pathogenic E. coli (ExPEC) infections, has been known widely for its contribution to the worldwide dissemination of multidrug resistance. Although other ExPEC-associated and ex...

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Autores principales:	Sabiha Shaik, Amit Ranjan, Sumeet K. Tiwari, Arif Hussain, Nishant Nandanwar, Narender Kumar, Savita Jadhav, Torsten Semmler, Ramani Baddam, Mohammed Aminul Islam, Munirul Alam, Lothar H. Wieler, Haruo Watanabe, Niyaz Ahmed
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2017
Materias:	bacterial evolution Escherichia coli genomics ST131 lineage molecular epidemiology Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/45493efb8ca9421cb6cf9ea5b4ae5b0c
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spelling	oai:doaj.org-article:45493efb8ca9421cb6cf9ea5b4ae5b0c2021-11-15T15:51:51ZComparative Genomic Analysis of Globally Dominant ST131 Clone with Other Epidemiologically Successful Extraintestinal Pathogenic <italic toggle="yes">Escherichia coli</italic> (ExPEC) Lineages10.1128/mBio.01596-172150-7511https://doaj.org/article/45493efb8ca9421cb6cf9ea5b4ae5b0c2017-11-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mBio.01596-17https://doaj.org/toc/2150-7511ABSTRACT Escherichia coli sequence type 131 (ST131), a pandemic clone responsible for the high incidence of extraintestinal pathogenic E. coli (ExPEC) infections, has been known widely for its contribution to the worldwide dissemination of multidrug resistance. Although other ExPEC-associated and extended-spectrum-β-lactamase (ESBL)-producing E. coli clones, such as ST38, ST405, and ST648 have been studied widely, no comparative genomic data with respect to other genotypes exist for ST131. In this study, comparative genomic analysis was performed for 99 ST131 E. coli strains with 40 genomes from three other STs, including ST38 (n = 12), ST405 (n = 10), and ST648 (n = 18), and functional studies were performed on five in-house strains corresponding to the four STs. Phylogenomic analysis results from this study corroborated with the sequence type-specific clonality. Results from the genome-wide resistance profiling confirmed that all strains were inherently multidrug resistant. ST131 genomes showed unique virulence profiles, and analysis of mobile genetic elements and their associated methyltransferases (MTases) has revealed that several of them were missing from the majority of the non-ST131 strains. Despite the fact that non-ST131 strains lacked few essential genes belonging to the serum resistome, the in-house strains representing all four STs demonstrated similar resistance levels to serum antibactericidal activity. Core genome analysis data revealed that non-ST131 strains usually lacked several ST131-defined genomic coordinates, and a significant number of genes were missing from the core of the ST131 genomes. Data from this study reinforce adaptive diversification of E. coli strains belonging to the ST131 lineage and provide new insights into the molecular mechanisms underlying clonal diversification of the ST131 lineage. IMPORTANCE E. coli, particularly the ST131 extraintestinal pathogenic E. coli (ExPEC) lineage, is an important cause of community- and hospital-acquired infections, such as urinary tract infections, surgical site infections, bloodstream infections, and sepsis. The treatment of infections caused by ExPEC has become very challenging due to the emergence of resistance to the first-line as well as the last-resort antibiotics. This study analyzes E. coli ST131 against three other important and globally distributed ExPEC lineages (ST38, ST405, and ST648) that also produced extended-spectrum β-lactamase (ESBL). This is perhaps the first study that employs the high-throughput whole-genome sequence-based approach to compare and study the genomic features of these four ExPEC lineages in relation to their functional properties. Findings from this study highlight the differences in the genomic coordinates of ST131 with respect to the other STs considered here. Results from this comparative genomics study can help in advancing the understanding of ST131 evolution and also offer a framework towards future developments in pathogen identification and targeted therapeutics to prevent diseases caused by this pandemic E. coli ST131 clone.Sabiha ShaikAmit RanjanSumeet K. TiwariArif HussainNishant NandanwarNarender KumarSavita JadhavTorsten SemmlerRamani BaddamMohammed Aminul IslamMunirul AlamLothar H. WielerHaruo WatanabeNiyaz AhmedAmerican Society for Microbiologyarticlebacterial evolutionEscherichia coligenomicsST131 lineagemolecular epidemiologyMicrobiologyQR1-502ENmBio, Vol 8, Iss 5 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	bacterial evolution Escherichia coli genomics ST131 lineage molecular epidemiology Microbiology QR1-502
spellingShingle	bacterial evolution Escherichia coli genomics ST131 lineage molecular epidemiology Microbiology QR1-502 Sabiha Shaik Amit Ranjan Sumeet K. Tiwari Arif Hussain Nishant Nandanwar Narender Kumar Savita Jadhav Torsten Semmler Ramani Baddam Mohammed Aminul Islam Munirul Alam Lothar H. Wieler Haruo Watanabe Niyaz Ahmed Comparative Genomic Analysis of Globally Dominant ST131 Clone with Other Epidemiologically Successful Extraintestinal Pathogenic <italic toggle="yes">Escherichia coli</italic> (ExPEC) Lineages
description	ABSTRACT Escherichia coli sequence type 131 (ST131), a pandemic clone responsible for the high incidence of extraintestinal pathogenic E. coli (ExPEC) infections, has been known widely for its contribution to the worldwide dissemination of multidrug resistance. Although other ExPEC-associated and extended-spectrum-β-lactamase (ESBL)-producing E. coli clones, such as ST38, ST405, and ST648 have been studied widely, no comparative genomic data with respect to other genotypes exist for ST131. In this study, comparative genomic analysis was performed for 99 ST131 E. coli strains with 40 genomes from three other STs, including ST38 (n = 12), ST405 (n = 10), and ST648 (n = 18), and functional studies were performed on five in-house strains corresponding to the four STs. Phylogenomic analysis results from this study corroborated with the sequence type-specific clonality. Results from the genome-wide resistance profiling confirmed that all strains were inherently multidrug resistant. ST131 genomes showed unique virulence profiles, and analysis of mobile genetic elements and their associated methyltransferases (MTases) has revealed that several of them were missing from the majority of the non-ST131 strains. Despite the fact that non-ST131 strains lacked few essential genes belonging to the serum resistome, the in-house strains representing all four STs demonstrated similar resistance levels to serum antibactericidal activity. Core genome analysis data revealed that non-ST131 strains usually lacked several ST131-defined genomic coordinates, and a significant number of genes were missing from the core of the ST131 genomes. Data from this study reinforce adaptive diversification of E. coli strains belonging to the ST131 lineage and provide new insights into the molecular mechanisms underlying clonal diversification of the ST131 lineage. IMPORTANCE E. coli, particularly the ST131 extraintestinal pathogenic E. coli (ExPEC) lineage, is an important cause of community- and hospital-acquired infections, such as urinary tract infections, surgical site infections, bloodstream infections, and sepsis. The treatment of infections caused by ExPEC has become very challenging due to the emergence of resistance to the first-line as well as the last-resort antibiotics. This study analyzes E. coli ST131 against three other important and globally distributed ExPEC lineages (ST38, ST405, and ST648) that also produced extended-spectrum β-lactamase (ESBL). This is perhaps the first study that employs the high-throughput whole-genome sequence-based approach to compare and study the genomic features of these four ExPEC lineages in relation to their functional properties. Findings from this study highlight the differences in the genomic coordinates of ST131 with respect to the other STs considered here. Results from this comparative genomics study can help in advancing the understanding of ST131 evolution and also offer a framework towards future developments in pathogen identification and targeted therapeutics to prevent diseases caused by this pandemic E. coli ST131 clone.
format	article
author	Sabiha Shaik Amit Ranjan Sumeet K. Tiwari Arif Hussain Nishant Nandanwar Narender Kumar Savita Jadhav Torsten Semmler Ramani Baddam Mohammed Aminul Islam Munirul Alam Lothar H. Wieler Haruo Watanabe Niyaz Ahmed
author_facet	Sabiha Shaik Amit Ranjan Sumeet K. Tiwari Arif Hussain Nishant Nandanwar Narender Kumar Savita Jadhav Torsten Semmler Ramani Baddam Mohammed Aminul Islam Munirul Alam Lothar H. Wieler Haruo Watanabe Niyaz Ahmed
author_sort	Sabiha Shaik
title	Comparative Genomic Analysis of Globally Dominant ST131 Clone with Other Epidemiologically Successful Extraintestinal Pathogenic <italic toggle="yes">Escherichia coli</italic> (ExPEC) Lineages
title_short	Comparative Genomic Analysis of Globally Dominant ST131 Clone with Other Epidemiologically Successful Extraintestinal Pathogenic <italic toggle="yes">Escherichia coli</italic> (ExPEC) Lineages
title_full	Comparative Genomic Analysis of Globally Dominant ST131 Clone with Other Epidemiologically Successful Extraintestinal Pathogenic <italic toggle="yes">Escherichia coli</italic> (ExPEC) Lineages
title_fullStr	Comparative Genomic Analysis of Globally Dominant ST131 Clone with Other Epidemiologically Successful Extraintestinal Pathogenic <italic toggle="yes">Escherichia coli</italic> (ExPEC) Lineages
title_full_unstemmed	Comparative Genomic Analysis of Globally Dominant ST131 Clone with Other Epidemiologically Successful Extraintestinal Pathogenic <italic toggle="yes">Escherichia coli</italic> (ExPEC) Lineages
title_sort	comparative genomic analysis of globally dominant st131 clone with other epidemiologically successful extraintestinal pathogenic <italic toggle="yes">escherichia coli</italic> (expec) lineages
publisher	American Society for Microbiology
publishDate	2017
url	https://doaj.org/article/45493efb8ca9421cb6cf9ea5b4ae5b0c
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Comparative Genomic Analysis of Globally Dominant ST131 Clone with Other Epidemiologically Successful Extraintestinal Pathogenic <italic toggle="yes">Escherichia coli</italic> (ExPEC) Lineages

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