Phylogenetic Analysis Reveals Distinct Evolutionary Trajectories of the Fluoroquinolones-Resistant Escherichia coli ST1193 From Fuzhou, China

Escherichia coli (E. coli) ST1193 is an emerging fluoroquinolones-resistant and virulent lineage. Large gaps remain in our understanding of the evolutionary processes and differences of this lineage. Therefore, we used 76 E. coli ST1193 genomes to detect strain-level genetic diversity and phylogeny...

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Autores principales:	Jiangqing Huang, Zhichang Zhao, Qianwen Zhang, Shengcen Zhang, Shuyu Zhang, Min Chen, Hongqiang Qiu, Yingping Cao, Bin Li
Formato:	article
Lenguaje:	EN
Publicado:	Frontiers Media S.A. 2021
Materias:	E. coli ST1193 whole genome sequencing phylogenomic analysis blaCTX–M–55 fluoroquinolones-resistant Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/a2815f3e6ba7443081c392d34f991b54
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spelling	oai:doaj.org-article:a2815f3e6ba7443081c392d34f991b542021-11-05T14:32:28ZPhylogenetic Analysis Reveals Distinct Evolutionary Trajectories of the Fluoroquinolones-Resistant Escherichia coli ST1193 From Fuzhou, China1664-302X10.3389/fmicb.2021.746995https://doaj.org/article/a2815f3e6ba7443081c392d34f991b542021-11-01T00:00:00Zhttps://www.frontiersin.org/articles/10.3389/fmicb.2021.746995/fullhttps://doaj.org/toc/1664-302XEscherichia coli (E. coli) ST1193 is an emerging fluoroquinolones-resistant and virulent lineage. Large gaps remain in our understanding of the evolutionary processes and differences of this lineage. Therefore, we used 76 E. coli ST1193 genomes to detect strain-level genetic diversity and phylogeny of this lineage globally. All E. coli ST1193 possessed fimH64, filCH5, and fumC14. There was 94.7% of isolates classified as O-type O75. There was 9.33% of E. coli ST1193 that possessed K5 capsular, while 90.67% of isolates possessed K1 capsular. The core genome analysis revealed that all isolates were divided into two phylogenetic clades (clade A and B). Clade A included 25 non-Chinese E. coli ST1193, and clade B contained all isolates collected from Fuzhou, China, respectively. The results of comparative genomics indicated Indels were identified in 150 clade-specific genes, which were enriched into the biological process and molecular function. Accessory genome phylogenetic tree showed a high degree of correlation between accessory genome clusters and core genome clades. There was significant difference in antibiotic resistance genes (ARGs) [blaCTX–M–55, blaTEM–1, sul2, tet(B), tet(R), APH(6)-Id, and AAC(3)-IId], virulence factors (cia, neuC, gad, and traT), and plasmid replicon types (IncQ1, Col156, and IncB/O/K/Z) between clade A (non-Chinese isolates) and clade B (Chinese isolates) (p < 0.05). Further analysis of the genetic environments of blaCTX–M–55 demonstrated that the flanking contexts of blaCTX–M–55 were diverse. In conclusion, our results reveal the distinct evolutionary trajectories of the spread of E. coli ST1193 in Fuzhou, China and non-China regions. This supports both global transmission and localized lineage expansion of this lineage following specific introductions into a geographic locality.Jiangqing HuangZhichang ZhaoQianwen ZhangShengcen ZhangShuyu ZhangMin ChenHongqiang QiuYingping CaoBin LiFrontiers Media S.A.articleE. coliST1193whole genome sequencingphylogenomic analysisblaCTX–M–55fluoroquinolones-resistantMicrobiologyQR1-502ENFrontiers in Microbiology, Vol 12 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	E. coli ST1193 whole genome sequencing phylogenomic analysis blaCTX–M–55 fluoroquinolones-resistant Microbiology QR1-502
spellingShingle	E. coli ST1193 whole genome sequencing phylogenomic analysis blaCTX–M–55 fluoroquinolones-resistant Microbiology QR1-502 Jiangqing Huang Zhichang Zhao Qianwen Zhang Shengcen Zhang Shuyu Zhang Min Chen Hongqiang Qiu Yingping Cao Bin Li Phylogenetic Analysis Reveals Distinct Evolutionary Trajectories of the Fluoroquinolones-Resistant Escherichia coli ST1193 From Fuzhou, China
description	Escherichia coli (E. coli) ST1193 is an emerging fluoroquinolones-resistant and virulent lineage. Large gaps remain in our understanding of the evolutionary processes and differences of this lineage. Therefore, we used 76 E. coli ST1193 genomes to detect strain-level genetic diversity and phylogeny of this lineage globally. All E. coli ST1193 possessed fimH64, filCH5, and fumC14. There was 94.7% of isolates classified as O-type O75. There was 9.33% of E. coli ST1193 that possessed K5 capsular, while 90.67% of isolates possessed K1 capsular. The core genome analysis revealed that all isolates were divided into two phylogenetic clades (clade A and B). Clade A included 25 non-Chinese E. coli ST1193, and clade B contained all isolates collected from Fuzhou, China, respectively. The results of comparative genomics indicated Indels were identified in 150 clade-specific genes, which were enriched into the biological process and molecular function. Accessory genome phylogenetic tree showed a high degree of correlation between accessory genome clusters and core genome clades. There was significant difference in antibiotic resistance genes (ARGs) [blaCTX–M–55, blaTEM–1, sul2, tet(B), tet(R), APH(6)-Id, and AAC(3)-IId], virulence factors (cia, neuC, gad, and traT), and plasmid replicon types (IncQ1, Col156, and IncB/O/K/Z) between clade A (non-Chinese isolates) and clade B (Chinese isolates) (p < 0.05). Further analysis of the genetic environments of blaCTX–M–55 demonstrated that the flanking contexts of blaCTX–M–55 were diverse. In conclusion, our results reveal the distinct evolutionary trajectories of the spread of E. coli ST1193 in Fuzhou, China and non-China regions. This supports both global transmission and localized lineage expansion of this lineage following specific introductions into a geographic locality.
format	article
author	Jiangqing Huang Zhichang Zhao Qianwen Zhang Shengcen Zhang Shuyu Zhang Min Chen Hongqiang Qiu Yingping Cao Bin Li
author_facet	Jiangqing Huang Zhichang Zhao Qianwen Zhang Shengcen Zhang Shuyu Zhang Min Chen Hongqiang Qiu Yingping Cao Bin Li
author_sort	Jiangqing Huang
title	Phylogenetic Analysis Reveals Distinct Evolutionary Trajectories of the Fluoroquinolones-Resistant Escherichia coli ST1193 From Fuzhou, China
title_short	Phylogenetic Analysis Reveals Distinct Evolutionary Trajectories of the Fluoroquinolones-Resistant Escherichia coli ST1193 From Fuzhou, China
title_full	Phylogenetic Analysis Reveals Distinct Evolutionary Trajectories of the Fluoroquinolones-Resistant Escherichia coli ST1193 From Fuzhou, China
title_fullStr	Phylogenetic Analysis Reveals Distinct Evolutionary Trajectories of the Fluoroquinolones-Resistant Escherichia coli ST1193 From Fuzhou, China
title_full_unstemmed	Phylogenetic Analysis Reveals Distinct Evolutionary Trajectories of the Fluoroquinolones-Resistant Escherichia coli ST1193 From Fuzhou, China
title_sort	phylogenetic analysis reveals distinct evolutionary trajectories of the fluoroquinolones-resistant escherichia coli st1193 from fuzhou, china
publisher	Frontiers Media S.A.
publishDate	2021
url	https://doaj.org/article/a2815f3e6ba7443081c392d34f991b54
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Phylogenetic Analysis Reveals Distinct Evolutionary Trajectories of the Fluoroquinolones-Resistant Escherichia coli ST1193 From Fuzhou, China

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