Cefotaxime (CTX) is a commonly used third-generation cephalosporin (3GC) to treat infections caused by Escherichia coil. Two genetic mechanisms have been associated with 3GC resistance in E. coli. The first is the conjugative transfer of a plasmid harboring antibiotic resistance genes. The second is the introduction of mutations in the promoter region of the ampC β-lactamase gene that cause chromosomal-encoded β-lactamase hyperproduction. A wide variety of promoter mutations related to AmpC hyperproduction have been described. However, their link to a specific 3GC such as CTX resistance has not been reported. Here, we measured CTX MICs in 172 cefoxitin resistant E. coli isolates and performed genome-wide analysis of homoplastic mutations associated with CTX resistance by comparing Illumina whole-genome sequencing data of all isolates to a PacBio tailored-made reference chromosome. We mapped the mutations on the reference chromosome and determined their occurrence in the phylogeny, revealing extreme homoplasy at the -42 position of the ampC promoter. The 24 occurrences of a 'T' at the -42 position rather than the wild type 'C', resulted from 18 independent C>T mutations in 5 phylogroups. The -42 C>T mutation was only observed in E. coli lacking a plasmid-encoded ampC gene. The association of the -42 C>T mutation with CTX resistance was confirmed to be significant (FDR < 0.05). To conclude, genome-wide analysis of homoplasy in combination with CTX resistance identifies the -42 C>T mutation of the ampC promotor as significantly associated with CTX resistance and underline the role of recurrent mutations in the spread of antibiotics resistance.

中文翻译：

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大肠杆菌中的全基因组分析揭示了与头孢噻肟抗性相关的遗传同质体水平达到前所未有的水平。

头孢噻肟（CTX）是常用的第三代头孢菌素（3GC），用于治疗由大肠杆菌引起的感染。大肠杆菌的3GC耐药与两种遗传机制有关。首先是带有抗生素抗性基因的质粒的结合转移。第二种是在ampCβ-内酰胺酶基因的启动子区域引入突变，这些突变会导致染色体编码的β-内酰胺酶高产。已经描述了与AmpC过度产生有关的多种启动子突变。但是，它们尚未与特定的3GC（例如CTX抗性）相关联。在这里，我们测量了172种耐头孢西丁的大肠杆菌中的CTX MIC通过将所有分离株的Illumina全基因组测序数据与PacBio量身定制的参考染色体进行比较，对与CTX抗性相关的同型突变进行分离并进行了全基因组分析。我们在参考染色体上绘制了突变图谱，并确定了它们在系统发育中的发生，揭示了在ampC启动子的-42位置处的极端同源性。在-42位而不是野生型'C'处有24个'T'发生是由5个系统组的18个独立C> T突变引起的。仅在缺乏质粒编码的ampC基因的大肠杆菌中观察到-42 C> T突变。证实-42 C> T突变与CTX耐药性之间存在显着相关性（FDR <0.05）。总而言之，对全基因组与CTX抗性相结合的全基因组分析确定ampC启动子的-42 C> T突变与CTX抗性显着相关，并强调了反复突变在抗生素抗性传播中的作用。