Inter-species geographic signatures for tracing horizontal gene transfer and long-term persistence of carbapenem resistance.
Inter-species geographic signatures for tracing horizontal gene transfer and long-term persistence of carbapenem resistance.
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DOI：
10.1186/s13073-022-01040-y
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发表时间：
2022-04-05
期刊：
影响因子：
12.3
通讯作者：
Earl AM
中科院分区：
文献类型：
--
作者：
Salamzade R;Manson AL;Walker BJ;Brennan-Krohn T;Worby CJ;Ma P;He LL;Shea TP;Qu J;Chapman SB;Howe W;Young SK;Wurster JI;Delaney ML;Kanjilal S;Onderdonk AB;Bittencourt CE;Gussin GM;Kim D;Peterson EM;Ferraro MJ;Hooper DC;Shenoy ES;Cuomo CA;Cosimi LA;Huang SS;Kirby JE;Pierce VM;Bhattacharyya RP;Earl AM
耐碳青霉烯肠杆菌（CRE）是一个紧迫的全球健康威胁。推断本地CRE传播的动态目前受到限制，因为我们无法自信地追踪耐药性决定因素向不相关的细菌宿主的传播。全基因组序列比较有助于识别CRE克隆传播和暴发，但碳青霉烯类耐药基因的高频水平基因转移（HGT）和随后的基因组重排使追踪这些基因在生物体中的局部持久性和动员变得复杂。为了克服这一限制，我们开发了一种新的方法来识别跨物种边界的大的、几乎相同的质粒片段的近期HGT，这也使我们能够克服基因组组装的技术挑战。我们将其应用于完整和接近完整的基因组组装，在近5年内从美国四家医院的患者中分离出的所有CRE以及时间和物种匹配的碳青霉烯类敏感肠杆菌的系统，前瞻性收集中检查CRE的局部传播。我们收集的CRE包括多种物种、谱系和碳青霉烯抗性机制，其中许多是在各种混杂质粒类型上编码的。我们发现并量化了质粒片段的重排、持久性和重复转移，包括那些含有碳青霉烯酶的质粒片段，多年来在生物体之间。一些质粒片段被发现与特定的区域密切相关，因此代表了地理特征，使得追踪最近和本地化的HGT事件成为可能。对这些特征的功能分析揭示了在医院病原体质粒中常见的基因，例如质粒保留和扩散所需的功能，以及对医院环境中常见的各种抗生素和防腐剂的生存。总的来说，我们开发的框架为抗生素耐药性在患者和医疗保健网络中的输入、传播和持续的流行病学提供了更清晰、高分辨率的图像。在线版本包含补充材料，可在10.1186/s13073-022-01040-y获得。
Carbapenem-resistant Enterobacterales (CRE) are an urgent global health threat. Inferring the dynamics of local CRE dissemination is currently limited by our inability to confidently trace the spread of resistance determinants to unrelated bacterial hosts. Whole-genome sequence comparison is useful for identifying CRE clonal transmission and outbreaks, but high-frequency horizontal gene transfer (HGT) of carbapenem resistance genes and subsequent genome rearrangement complicate tracing the local persistence and mobilization of these genes across organisms. To overcome this limitation, we developed a new approach to identify recent HGT of large, near-identical plasmid segments across species boundaries, which also allowed us to overcome technical challenges with genome assembly. We applied this to complete and near-complete genome assemblies to examine the local spread of CRE in a systematic, prospective collection of all CRE, as well as time- and species-matched carbapenem-susceptible Enterobacterales, isolated from patients from four US hospitals over nearly 5 years. Our CRE collection comprised a diverse range of species, lineages, and carbapenem resistance mechanisms, many of which were encoded on a variety of promiscuous plasmid types. We found and quantified rearrangement, persistence, and repeated transfer of plasmid segments, including those harboring carbapenemases, between organisms over multiple years. Some plasmid segments were found to be strongly associated with specific locales, thus representing geographic signatures that make it possible to trace recent and localized HGT events. Functional analysis of these signatures revealed genes commonly found in plasmids of nosocomial pathogens, such as functions required for plasmid retention and spread, as well survival against a variety of antibiotic and antiseptics common to the hospital environment. Collectively, the framework we developed provides a clearer, high-resolution picture of the epidemiology of antibiotic resistance importation, spread, and persistence in patients and healthcare networks. The online version contains supplementary material available at 10.1186/s13073-022-01040-y.
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DOI：
10.1016/j.cmi.2016.09.003
发表时间：
2017-01
期刊：
Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases
影响因子：
--
作者：
Bartsch SM;McKinnell JA;Mueller LE;Miller LG;Gohil SK;Huang SS;Lee BY
通讯作者：
Lee BY
Biopython：用于计算分子生物学和生物信息学的免费 Python 工具。
DOI：
10.1093/bioinformatics/btp163
发表时间：
2009-06-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Cock PJ;Antao T;Chang JT;Chapman BA;Cox CJ;Dalke A;Friedberg I;Hamelryck T;Kauff F;Wilczynski B;de Hoon MJ
通讯作者：
de Hoon MJ
影响因子：
3.7
作者：
Abby SS;Néron B;Ménager H;Touchon M;Rocha EP
通讯作者：
Rocha EP
影响因子：
4.5
作者：
Chitnis, Amit S.;Caruthers, Pam S.;Wise, Matthew E.
通讯作者：
Wise, Matthew E.
影响因子：
17.1
作者：
Conlan S;Thomas PJ;Deming C;Park M;Lau AF;Dekker JP;Snitkin ES;Clark TA;Luong K;Song Y;Tsai YC;Boitano M;Dayal J;Brooks SY;Schmidt B;Young AC;Thomas JW;Bouffard GG;Blakesley RW;NISC Comparative Sequencing Program;Mullikin JC;Korlach J;Henderson DK;Frank KM;Palmore TN;Segre JA
通讯作者：
Segre JA