Zeng Xiancheng, Chi Xuelin, Ho Brian T, Moon Damee, Lambert Christine, Hall Richard J, Baybayan Primo, Wang Shihua, Wilson Brenda A, Ho Mengfei
Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, China.
College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China.
mSystems. 2019 Feb 26;4(1). doi: 10.1128/mSystems.00242-18. eCollection 2019 Jan-Feb.
Extensive drug resistance (XDR) is an escalating global problem. Escherichia coli strain Sanji was isolated from an outbreak of pheasant colibacillosis in Fujian province, China, in 2011. This strain has XDR properties, exhibiting sensitivity to carbapenems but no other classes of known antibiotics. Whole-genome sequencing revealed a total of 32 known antibiotic resistance genes, many associated with insertion sequence 26 (IS) elements. These were found on the Sanji chromosome and 2 of its 6 plasmids, pSJ_255 and pSJ_82. The Sanji chromosome also harbors a type 2 secretion system (T2SS), a type 3 secretion system (T3SS), a type 6 secretion system (T6SS), and several putative prophages. Sanji and other ST167 strains have a previously uncharacterized O-antigen (O89b) that is most closely related to serotype O89 as determined on the basis of analysis of the genes and serotyping. This O89b-antigen gene cluster was also found in the genomes of a few other pathogenic sequence type 617 (ST617) and ST10 complex strains. A time-scaled phylogeny inferred from comparative single nucleotide variant analysis indicated that development of these O89b-containing lineages emerged about 30 years ago. Comparative sequence analysis revealed that the core genome of Sanji is nearly identical to that of several recently sequenced strains of pathogenic XDR E. coli belonging to the ST167 group. Comparison of the mobile elements among the different ST167 genomes revealed that each genome carries a distinct set of multidrug resistance genes on different types of plasmids, indicating that there are multiple paths toward the emergence of XDR in E. coli. E. coli strain Sanji is the first sequenced and analyzed genome of the recently emerged pathogenic XDR strains with sequence type ST167 and novel serotype O89b:H9. Comparison of the genomes of Sanji with other ST167 strains revealed distinct sets of different plasmids, mobile IS elements, and antibiotic resistance genes in each genome, indicating that there exist multiple paths toward achieving XDR. The emergence of these pathogenic ST167 E. coli strains with diverse XDR capabilities highlights the difficulty of preventing or mitigating the development of XDR properties in bacteria and points to the importance of better understanding of the shared underlying virulence mechanisms and physiology of pathogenic bacteria.
广泛耐药（XDR）是一个日益严重的全球性问题。大肠杆菌菌株“三吉”于2011年在中国福建省一次雉鸡大肠杆菌病暴发中分离得到。该菌株具有XDR特性，对碳青霉烯类敏感，但对其他已知抗生素类别均不敏感。全基因组测序共发现32个已知的抗生素耐药基因，其中许多与插入序列26（IS）元件相关。这些基因存在于“三吉”菌株的染色体及其6个质粒中的2个（pSJ_255和pSJ_82）上。“三吉”菌株的染色体还含有一个2型分泌系统（T2SS）、一个3型分泌系统（T3SS）、一个6型分泌系统（T6SS）以及几个推定的原噬菌体。“三吉”菌株和其他ST167菌株具有一种以前未鉴定的O抗原（O89b），根据基因分析和血清分型确定，该抗原与血清型O89关系最为密切。在其他一些致病性序列类型617（ST617）和ST10复合体菌株的基因组中也发现了这种O89b抗原基因簇。通过比较单核苷酸变异分析推断的时间尺度系统发育表明，这些含O89b谱系大约在30年前出现。比较序列分析显示，“三吉”菌株的核心基因组与最近测序的几株属于ST167组的致病性XDR大肠杆菌菌株的核心基因组几乎相同。对不同ST167基因组中的移动元件进行比较发现，每个基因组在不同类型的质粒上携带一组不同的多重耐药基因，这表明大肠杆菌中XDR的出现有多种途径。大肠杆菌菌株“三吉”是最近出现的具有序列类型ST167和新型血清型O89b:H9的致病性XDR菌株中首个进行测序和分析的基因组。将“三吉”菌株的基因组与其他ST167菌株进行比较发现，每个基因组中存在不同的质粒、移动IS元件和抗生素耐药基因组合，这表明实现XDR有多种途径。这些具有不同XDR能力的致病性ST167大肠杆菌菌株的出现凸显了预防或减轻细菌中XDR特性发展的困难，并指出了更好地了解病原菌共同的潜在毒力机制和生理学的重要性。
