Sheppard Anna E, Stoesser Nicole, Wilson Daniel J, Sebra Robert, Kasarskis Andrew, Anson Luke W, Giess Adam, Pankhurst Louise J, Vaughan Alison, Grim Christopher J, Cox Heather L, Yeh Anthony J, Sifri Costi D, Walker A Sarah, Peto Tim E, Crook Derrick W, Mathers Amy J
Modernizing Medical Microbiology Consortium, Nuffield Department of Clinical Medicine, John Radcliffe Hospital, Oxford University, Oxford, United Kingdom
Modernizing Medical Microbiology Consortium, Nuffield Department of Clinical Medicine, John Radcliffe Hospital, Oxford University, Oxford, United Kingdom.
Antimicrob Agents Chemother. 2016 May 23;60(6):3767-78. doi: 10.1128/AAC.00464-16. Print 2016 Jun.
The recent widespread emergence of carbapenem resistance in Enterobacteriaceae is a major public health concern, as carbapenems are a therapy of last resort against this family of common bacterial pathogens. Resistance genes can mobilize via various mechanisms, including conjugation and transposition; however, the importance of this mobility in short-term evolution, such as within nosocomial outbreaks, is unknown. Using a combination of short- and long-read whole-genome sequencing of 281 blaKPC-positive Enterobacteriaceae isolates from a single hospital over 5 years, we demonstrate rapid dissemination of this carbapenem resistance gene to multiple species, strains, and plasmids. Mobility of blaKPC occurs at multiple nested genetic levels, with transmission of blaKPC strains between individuals, frequent transfer of blaKPC plasmids between strains/species, and frequent transposition of blaKPC transposon Tn4401 between plasmids. We also identify a common insertion site for Tn4401 within various Tn2-like elements, suggesting that homologous recombination between Tn2-like elements has enhanced the spread of Tn4401 between different plasmid vectors. Furthermore, while short-read sequencing has known limitations for plasmid assembly, various studies have attempted to overcome this by the use of reference-based methods. We also demonstrate that, as a consequence of the genetic mobility observed in this study, plasmid structures can be extremely dynamic, and therefore these reference-based methods, as well as traditional partial typing methods, can produce very misleading conclusions. Overall, our findings demonstrate that nonclonal resistance gene dissemination can be extremely rapid, presenting significant challenges for public health surveillance and achieving effective control of antibiotic resistance.
近年来，肠杆菌科细菌中碳青霉烯耐药性的广泛出现成为一个重大的公共卫生问题，因为碳青霉烯类药物是针对这类常见细菌病原体的最后一道治疗防线。耐药基因可通过多种机制移动，包括接合和转座；然而，这种移动性在短期进化（如医院内暴发期间）中的重要性尚不清楚。我们对一家医院5年内分离出的281株携带blaKPC的肠杆菌科细菌进行了短读长和长读长全基因组测序，结果表明该碳青霉烯耐药基因能迅速传播到多个菌种、菌株和质粒。blaKPC的移动发生在多个嵌套的遗传水平上，包括blaKPC菌株在个体间的传播、blaKPC质粒在菌株/菌种间的频繁转移以及blaKPC转座子Tn4401在质粒间的频繁转座。我们还在各种Tn2样元件中确定了Tn4401的一个共同插入位点，这表明Tn2样元件之间的同源重组增强了Tn4401在不同质粒载体之间的传播。此外，虽然短读长测序在质粒组装方面存在已知局限性，但各种研究已尝试通过基于参考的方法来克服这一问题。我们还证明，由于本研究中观察到的基因移动性，质粒结构可能极具动态性，因此这些基于参考的方法以及传统的部分分型方法可能会得出极具误导性的结论。总体而言，我们的研究结果表明，非克隆性耐药基因的传播可能极其迅速，这给公共卫生监测和有效控制抗生素耐药性带来了重大挑战。
