AUTHOR=Huang Jiangqing , Zhao Zhichang , Zhang Qianwen , Zhang Shengcen , Zhang Shuyu , Chen Min , Qiu Hongqiang , Cao Yingping , Li Bin 

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

JOURNAL=Frontiers in Microbiology

VOLUME=12

YEAR=2021

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2021.746995

DOI=10.3389/fmicb.2021.746995

ISSN=1664-302X

ABSTRACT=<p><italic>Escherichia coli</italic> (<italic>E. coli</italic>) 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 <italic>E. coli</italic> ST1193 genomes to detect strain-level genetic diversity and phylogeny of this lineage globally. All <italic>E. coli</italic> ST1193 possessed <italic>fimH64</italic>, <italic>filCH5</italic>, and <italic>fumC14</italic>. There was 94.7% of isolates classified as O-type O75. There was 9.33% of <italic>E. coli</italic> 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 <italic>E. coli</italic> 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) [<italic>bla</italic><sub><italic>CTX–M–55</italic></sub>, <italic>bla</italic><sub><italic>TEM–1</italic></sub>, <italic>sul2</italic>, <italic>tet(B)</italic>, <italic>tet(R)</italic>, <italic>APH(6)-Id</italic>, and <italic>AAC(3)-IId</italic>], virulence factors (<italic>cia</italic>, <italic>neuC</italic>, <italic>gad</italic>, and <italic>traT)</italic>, and plasmid replicon types (IncQ1, Col156, and IncB/O/K/Z) between clade A (non-Chinese isolates) and clade B (Chinese isolates) (<italic>p</italic> &lt; 0.05). Further analysis of the genetic environments of <italic>bla</italic><sub><italic>CTX–M–55</italic></sub> demonstrated that the flanking contexts of <italic>bla</italic><sub><italic>CTX–M–55</italic></sub> were diverse. In conclusion, our results reveal the distinct evolutionary trajectories of the spread of <italic>E. coli</italic> 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.</p>