National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.
Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China.
Genome Med. 2020 Dec 7;12(1):111. doi: 10.1186/s13073-020-00807-5.
The recent emergence and dissemination of high-level mobile tigecycline resistance Tet(X) challenge the clinical effectiveness of tigecycline, one of the last-resort therapeutic options for complicated infections caused by multidrug-resistant Gram-negative and Gram-positive pathogens. Although tet(X) has been found in various bacterial species, less is known about phylogeographic distribution and phenotypic variance of different genetic variants.
Herein, we conducted a multiregional whole-genome sequencing study of tet(X)-positive Acinetobacter isolates from human, animal, and their surrounding environmental sources in China. The molecular and enzymatic features of tet(X) variants were characterized by clonal expression, microbial degradation, reverse transcription, and gene transfer experiments, while the tet(X) genetic diversity and molecular evolution were explored by comparative genomic and Bayesian evolutionary analyses.
We identified 193 tet(X)-positive isolates from 3846 samples, with the prevalence ranging from 2.3 to 25.3% in nine provinces in China. The tet(X) was broadly distributed in 12 Acinetobacter species, including six novel species firstly described here. Besides tet(X3) (n = 188) and tet(X4) (n = 5), two tet(X5) variants, tet(X5.2) (n = 36) and tet(X5.3) (n = 4), were also found together with tet(X3) or tet(X4) but without additive effects on tetracyclines. These tet(X)-positive Acinetobacter spp. isolates exhibited 100% resistance rates to tigecycline and tetracycline, as well as high minimum inhibitory concentrations to eravacycline (2-8 μg/mL) and omadacycline (8-16 μg/mL). Genetic analysis revealed that different tet(X) variants shared an analogous ISCR2-mediated transposon structure. The molecular evolutionary analysis indicated that Tet(X) variants likely shared the same common ancestor with the chromosomal monooxygenases that are found in environmental Flavobacteriaceae bacteria, but sequence divergence suggested separation ~ 9900 years ago (7887 BC), presumably associated with the mobilization of tet(X)-like genes through horizontal transfer.
Four tet(X) variants were identified in this study, and they were widely distributed in multiple Acinetobacter spp. strains from various ecological niches across China. Our research also highlighted the crucial role of ISCR2 in mobilizing tet(X)-like genes between different Acinetobacter species and explored the evolutionary history of Tet(X)-like monooxygenases. Further studies are needed to evaluate the clinical impact of these mobile tigecycline resistance genes.
高水平移动替加环素耐药基因 Tet(X) 的出现和传播，对替加环素的临床疗效构成了挑战，替加环素是治疗多药耐药革兰氏阴性和革兰氏阳性病原体引起的复杂感染的最后手段之一。虽然已经在各种细菌物种中发现了 tet(X)，但关于不同遗传变异体的地理分布和表型差异知之甚少。
本研究对来自中国人类、动物及其周围环境来源的 tet(X) 阳性不动杆菌分离株进行了多区域全基因组测序研究。通过克隆表达、微生物降解、逆转录和基因转移实验，对 tet(X) 变体的分子和酶特性进行了表征，通过比较基因组和贝叶斯进化分析探索了 tet(X) 的遗传多样性和分子进化。
我们从 3846 个样本中鉴定出 193 株 tet(X) 阳性分离株，在中国 9 个省份的检出率为 2.3%至 25.3%。tet(X) 广泛分布于 12 种不动杆菌种，其中包括 6 种首次在此描述的新种。除了 tet(X3) (n=188) 和 tet(X4) (n=5)，还发现了两种 tet(X5) 变体 tet(X5.2) (n=36) 和 tet(X5.3) (n=4)，它们与 tet(X3) 或 tet(X4) 一起存在，但对四环素没有相加作用。这些 tet(X) 阳性不动杆菌属分离株对替加环素和四环素的耐药率均为 100%，对依拉环素（2-8μg/mL）和奥马环素（8-16μg/mL）的最小抑菌浓度也较高。遗传分析表明，不同的 tet(X) 变体共享一个类似的 ISCR2 介导的转座子结构。分子进化分析表明，Tet(X) 变体可能与环境黄杆菌科细菌中发现的染色体单加氧酶具有相同的共同祖先，但序列分歧表明它们大约在 9900 年前（公元前 7887 年）就已经分离，可能与通过水平转移移动 tet(X) 样基因有关。
本研究鉴定了 4 种 tet(X) 变体，它们广泛分布于来自中国不同生态位的多种不动杆菌属菌株中。我们的研究还强调了 ISCR2 在不同不动杆菌种之间移动 tet(X) 样基因中的关键作用，并探讨了 Tet(X) 样单加氧酶的进化历史。需要进一步研究来评估这些移动替加环素耐药基因的临床影响。
