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

Abstract

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