Supplementary Table S5. Conclusions of the phylogenetic reconstruction. from Gene sharing among plasmids and chromoomes reveals barriers for antibiotic resistance gene transfer

The emergence of antibiotic resistant bacteria is a major threat to modern medicine. Rapid adaptation to antibiotics is often mediated by the acquisition of plasmids carrying antibiotic resistance (ABR) genes. Nonetheless, the determinants of plasmid-mediated ABR gene transfer remain debated. Here, we show that the propensity of ABR gene transfer via plasmids is higher for accessory chromosomal ABR genes in comparison to core chromosomal ABR genes, regardless of the resistance mechanism. Analysing the pattern of ABR gene occurrence in the genomes of 2635 <i>Enterobacteriaceae</i> isolates, we find that 33% of the 416 ABR genes are shared between chromosomes and plasmids. Phylogenetic reconstruction of ABR genes occurring on both plasmids and chromosomes supports their evolution by lateral gene transfer. Furthermore, accessory ABR genes (encoded in less than 10% of the chromosomes) occur more abundantly in plasmids in comparison to core ABR genes (encoded in greater than or equal to 90% of the chromosomes). The pattern of ABR gene occurrence in plasmids and chromosomes is similar to the total <i>Escherichia</i> genome. Our results thus indicate that the previously recognized barriers for gene acquisition by lateral gene transfer apply also to ABR genes. We propose that the functional complexity of the underlying ABR mechanism is an important determinant of ABR gene transferability.This article is part of the theme issue ‘The secret lives of microbial mobile genetic elements’.

抗生素耐药细菌的出现是现代医学面临的重大威胁。细菌对抗生素的快速耐药性演化，通常通过获取携带抗生素耐药（ABR）基因的质粒得以介导。然而，质粒介导的ABR基因转移的决定因素仍存在广泛争议。本研究表明，无论耐药机制类型如何，附属染色体编码的ABR基因通过质粒发生转移的倾向，均显著高于核心染色体编码的ABR基因。通过分析2635株肠杆菌科（Enterobacteriaceae）分离株的基因组中ABR基因的分布模式，我们发现416个ABR基因中有33%同时存在于染色体与质粒中。对同时存在于质粒与染色体中的ABR基因进行系统发育重建，结果证实其演化过程伴随水平基因转移。此外，附属ABR基因（仅在≤10%的菌株染色体中编码）在质粒中的丰度显著高于核心ABR基因（在≥90%的菌株染色体中编码）。质粒与染色体中ABR基因的分布模式，与埃希氏菌属（Escherichia）的全基因组分布模式相似。综上，本研究结果表明，此前已被证实的、通过水平基因转移获取外源基因的障碍，同样适用于ABR基因。我们提出，ABR机制本身的功能复杂性是影响ABR基因可转移性的重要决定因素。本文属于“微生物可移动遗传元件的隐秘生命”专题议题的一部分。