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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) [ bla   CTX–M–55  ,  bla   TEM–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  bla   CTX–M–55   demonstrated that the flanking contexts of  bla   CTX–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.

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