Comparative Genome Analysis of an Extensively Drug-Resistant Isolate of Avian Sequence Type 167 <italic toggle="yes">Escherichia coli</italic> Strain Sanji with Novel <italic toggle="yes">In Silico</italic> Serotype O89b:H9

ABSTRACT Extensive drug resistance (XDR) is an escalating global problem. Escherichia coli strain Sanji was isolated from an outbreak of pheasant colibacillosis in Fujian province, China, in 2011. This strain has XDR properties, exhibiting sensitivity to carbapenems but no other classes of known ant...

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Autores principales:	Xiancheng Zeng, Xuelin Chi, Brian T. Ho, Damee Moon, Christine Lambert, Richard J. Hall, Primo Baybayan, Shihua Wang, Brenda A. Wilson, Mengfei Ho
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2019
Materias:	O-antigen antibiotic resistance capsular polysaccharide extensively drug resistant genome comparison insertion sequence Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/f144fc05d98445e0b640385f5a975dad
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spelling	oai:doaj.org-article:f144fc05d98445e0b640385f5a975dad2021-12-02T18:39:15ZComparative Genome Analysis of an Extensively Drug-Resistant Isolate of Avian Sequence Type 167 <italic toggle="yes">Escherichia coli</italic> Strain Sanji with Novel <italic toggle="yes">In Silico</italic> Serotype O89b:H910.1128/mSystems.00242-182379-5077https://doaj.org/article/f144fc05d98445e0b640385f5a975dad2019-02-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSystems.00242-18https://doaj.org/toc/2379-5077ABSTRACT Extensive drug resistance (XDR) is an escalating global problem. Escherichia coli strain Sanji was isolated from an outbreak of pheasant colibacillosis in Fujian province, China, in 2011. This strain has XDR properties, exhibiting sensitivity to carbapenems but no other classes of known antibiotics. Whole-genome sequencing revealed a total of 32 known antibiotic resistance genes, many associated with insertion sequence 26 (IS26) elements. These were found on the Sanji chromosome and 2 of its 6 plasmids, pSJ_255 and pSJ_82. The Sanji chromosome also harbors a type 2 secretion system (T2SS), a type 3 secretion system (T3SS), a type 6 secretion system (T6SS), and several putative prophages. Sanji and other ST167 strains have a previously uncharacterized O-antigen (O89b) that is most closely related to serotype O89 as determined on the basis of analysis of the wzm-wzt genes and in silico serotyping. This O89b-antigen gene cluster was also found in the genomes of a few other pathogenic sequence type 617 (ST617) and ST10 complex strains. A time-scaled phylogeny inferred from comparative single nucleotide variant analysis indicated that development of these O89b-containing lineages emerged about 30 years ago. Comparative sequence analysis revealed that the core genome of Sanji is nearly identical to that of several recently sequenced strains of pathogenic XDR E. coli belonging to the ST167 group. Comparison of the mobile elements among the different ST167 genomes revealed that each genome carries a distinct set of multidrug resistance genes on different types of plasmids, indicating that there are multiple paths toward the emergence of XDR in E. coli. IMPORTANCE E. coli strain Sanji is the first sequenced and analyzed genome of the recently emerged pathogenic XDR strains with sequence type ST167 and novel in silico serotype O89b:H9. Comparison of the genomes of Sanji with other ST167 strains revealed distinct sets of different plasmids, mobile IS elements, and antibiotic resistance genes in each genome, indicating that there exist multiple paths toward achieving XDR. The emergence of these pathogenic ST167 E. coli strains with diverse XDR capabilities highlights the difficulty of preventing or mitigating the development of XDR properties in bacteria and points to the importance of better understanding of the shared underlying virulence mechanisms and physiology of pathogenic bacteria. Author Video: An author video summary of this article is available.Xiancheng ZengXuelin ChiBrian T. HoDamee MoonChristine LambertRichard J. HallPrimo BaybayanShihua WangBrenda A. WilsonMengfei HoAmerican Society for MicrobiologyarticleO-antigenantibiotic resistancecapsular polysaccharideextensively drug resistantgenome comparisoninsertion sequenceMicrobiologyQR1-502ENmSystems, Vol 4, Iss 1 (2019)
institution	DOAJ
collection	DOAJ
language	EN
topic	O-antigen antibiotic resistance capsular polysaccharide extensively drug resistant genome comparison insertion sequence Microbiology QR1-502
spellingShingle	O-antigen antibiotic resistance capsular polysaccharide extensively drug resistant genome comparison insertion sequence Microbiology QR1-502 Xiancheng Zeng Xuelin Chi Brian T. Ho Damee Moon Christine Lambert Richard J. Hall Primo Baybayan Shihua Wang Brenda A. Wilson Mengfei Ho Comparative Genome Analysis of an Extensively Drug-Resistant Isolate of Avian Sequence Type 167 <italic toggle="yes">Escherichia coli</italic> Strain Sanji with Novel <italic toggle="yes">In Silico</italic> Serotype O89b:H9
description	ABSTRACT Extensive drug resistance (XDR) is an escalating global problem. Escherichia coli strain Sanji was isolated from an outbreak of pheasant colibacillosis in Fujian province, China, in 2011. This strain has XDR properties, exhibiting sensitivity to carbapenems but no other classes of known antibiotics. Whole-genome sequencing revealed a total of 32 known antibiotic resistance genes, many associated with insertion sequence 26 (IS26) elements. These were found on the Sanji chromosome and 2 of its 6 plasmids, pSJ_255 and pSJ_82. The Sanji chromosome also harbors a type 2 secretion system (T2SS), a type 3 secretion system (T3SS), a type 6 secretion system (T6SS), and several putative prophages. Sanji and other ST167 strains have a previously uncharacterized O-antigen (O89b) that is most closely related to serotype O89 as determined on the basis of analysis of the wzm-wzt genes and in silico serotyping. This O89b-antigen gene cluster was also found in the genomes of a few other pathogenic sequence type 617 (ST617) and ST10 complex strains. A time-scaled phylogeny inferred from comparative single nucleotide variant analysis indicated that development of these O89b-containing lineages emerged about 30 years ago. Comparative sequence analysis revealed that the core genome of Sanji is nearly identical to that of several recently sequenced strains of pathogenic XDR E. coli belonging to the ST167 group. Comparison of the mobile elements among the different ST167 genomes revealed that each genome carries a distinct set of multidrug resistance genes on different types of plasmids, indicating that there are multiple paths toward the emergence of XDR in E. coli. IMPORTANCE E. coli strain Sanji is the first sequenced and analyzed genome of the recently emerged pathogenic XDR strains with sequence type ST167 and novel in silico serotype O89b:H9. Comparison of the genomes of Sanji with other ST167 strains revealed distinct sets of different plasmids, mobile IS elements, and antibiotic resistance genes in each genome, indicating that there exist multiple paths toward achieving XDR. The emergence of these pathogenic ST167 E. coli strains with diverse XDR capabilities highlights the difficulty of preventing or mitigating the development of XDR properties in bacteria and points to the importance of better understanding of the shared underlying virulence mechanisms and physiology of pathogenic bacteria. Author Video: An author video summary of this article is available.
format	article
author	Xiancheng Zeng Xuelin Chi Brian T. Ho Damee Moon Christine Lambert Richard J. Hall Primo Baybayan Shihua Wang Brenda A. Wilson Mengfei Ho
author_facet	Xiancheng Zeng Xuelin Chi Brian T. Ho Damee Moon Christine Lambert Richard J. Hall Primo Baybayan Shihua Wang Brenda A. Wilson Mengfei Ho
author_sort	Xiancheng Zeng
title	Comparative Genome Analysis of an Extensively Drug-Resistant Isolate of Avian Sequence Type 167 <italic toggle="yes">Escherichia coli</italic> Strain Sanji with Novel <italic toggle="yes">In Silico</italic> Serotype O89b:H9
title_short	Comparative Genome Analysis of an Extensively Drug-Resistant Isolate of Avian Sequence Type 167 <italic toggle="yes">Escherichia coli</italic> Strain Sanji with Novel <italic toggle="yes">In Silico</italic> Serotype O89b:H9
title_full	Comparative Genome Analysis of an Extensively Drug-Resistant Isolate of Avian Sequence Type 167 <italic toggle="yes">Escherichia coli</italic> Strain Sanji with Novel <italic toggle="yes">In Silico</italic> Serotype O89b:H9
title_fullStr	Comparative Genome Analysis of an Extensively Drug-Resistant Isolate of Avian Sequence Type 167 <italic toggle="yes">Escherichia coli</italic> Strain Sanji with Novel <italic toggle="yes">In Silico</italic> Serotype O89b:H9
title_full_unstemmed	Comparative Genome Analysis of an Extensively Drug-Resistant Isolate of Avian Sequence Type 167 <italic toggle="yes">Escherichia coli</italic> Strain Sanji with Novel <italic toggle="yes">In Silico</italic> Serotype O89b:H9
title_sort	comparative genome analysis of an extensively drug-resistant isolate of avian sequence type 167 <italic toggle="yes">escherichia coli</italic> strain sanji with novel <italic toggle="yes">in silico</italic> serotype o89b:h9
publisher	American Society for Microbiology
publishDate	2019
url	https://doaj.org/article/f144fc05d98445e0b640385f5a975dad
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Comparative Genome Analysis of an Extensively Drug-Resistant Isolate of Avian Sequence Type 167 <italic toggle="yes">Escherichia coli</italic> Strain Sanji with Novel <italic toggle="yes">In Silico</italic> Serotype O89b:H9

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