Genomic Insights into Global blaCTX-M-55-Positive Escherichia coli Epidemiology and Transmission Characteristics

Abstract

In recent years, bla_CTX-M-55-positive Escherichia coli has been widely reported in multiple locations with an increasing trend in prevalence, yet few studies have comprehensively analyzed the transmission characteristics and epidemiological patterns of bla_CTX-M-55-positive E. coli. Here, we constructed a bla_CTX-M-55-positive E. coli global genomic data set as completely as possible and explored the epidemiology and potential impact of bla_CTX-M-55-positive E. coli on a global scale by high-resolution bioinformatics methods. The results show that bla_CTX-M-55-positive E. coli has spread widely worldwide, especially in Asia, with the rich sequence typing (ST) diversity and high proportion of auxiliary genome occupancy indicating a high degree of openness. The phylogenetic tree suggests that bla_CTX-M-55-positive E. coli is frequently clonally transmitted between the three human-animal environments and often cotransmitted with fosA, mcr, bla_NDM, and tet(X). The stable presence of InclI1 and InclI2 in different hosts from different sources suggests that this part of the plasmid drives the widespread transmission of bla_CTX-M-55-positive E. coli. We inductively clustered all bla_CTX-M-55 flanking environmental gene structures and obtained five types. Notably, "ISEcp1-bla_CTX-M-55-orf477-(Tn2)" and "IS26(IS15DI)-hp-hp-bla_CTX-M-55-orf477-hp-bla_TEM-IS26-hp-IS26-Tn2" are dominant in "humans" and in "animals and related foods," respectively. Overall, our findings highlight the importance of whole-genome sequencing-based surveillance in exploring the transmission and evolution of bla_CTX-M-55-positive E. coli in the context of "One Health," and they serve as a reminder to strengthen the surveillance of bla_CTX-M-55-positive E. coli in order to address the potential risk of future large outbreaks. IMPORTANCE CTX-M-55 was first discovered in Thailand in 2004, and today, this enzyme is the most common CTX-M subtype in E. coli of animal origin in China. Thus, bla_CTX-M-55-positive E. coli getting widely spread is a growing public health problem. Although prevalence surveys of bla_CTX-M-55-positive E. coli in different hosts have been widely reported in recent years, they remain insufficient in "One Health" context and from a global comprehensive perspective. Here, we constructed a genomic database of 2144 bla_CTX-M-55-positive E. coli and used bioinformatics methods to resolve the spread and evolution of bla_CTX-M-55-positive E. coli. The results suggest a potential risk of rapid transmission of bla_CTX-M-55-positive E. coli and that long-term continuous surveillance of bla_CTX-M-55-positive E. coli should be emphasized.

Keywords: Escherichia coli; blaCTX-M-55; plasmid; whole-genome sequencing.