Genome of the pathogen Porphyromonas gingivalis recovered from a biofilm in a hospital sink using a high-throughput single-cell genomics platform.
Genome of the pathogen Porphyromonas gingivalis recovered from a biofilm in a hospital sink using a high-throughput single-cell genomics platform.
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DOI：
10.1101/gr.150433.112
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发表时间：
2013-05
期刊：
影响因子：
7
通讯作者：
Lasken RS
中科院分区：
文献类型：
--
作者：
McLean JS;Lombardo MJ;Ziegler MG;Novotny M;Yee-Greenbaum J;Badger JH;Tesler G;Nurk S;Lesin V;Brami D;Hall AP;Edlund A;Allen LZ;Durkin S;Reed S;Torriani F;Nealson KH;Pevzner PA;Friedman R;Venter JC;Lasken RS
虽然生物膜已被证明是病原体的水库，我们的知识的生物膜中的微生物多样性的关键领域，如医疗保健设施，是有限的。用于病原体鉴定和菌株分型的可用方法具有一些固有的限制。特别是，培养只会产生一小部分存在的物种，毒力或标记基因的PCR主要集中在少数已知物种上，而鸟枪宏基因组学在检测菌株变异的能力方面受到限制。在这项研究中，我们提出了一种单细胞基因组测序方法来解决这些限制，并通过专门针对医院浴室水槽排水管中复杂生物膜内的细菌细胞来证明这一点。一种新开发的自动化平台用于通过多重置换扩增（MDA）技术从数百个单细胞平行产生基因组DNA。MDA反应进行筛选和分类的16S rRNA基因PCR序列，揭示了广泛的细菌，涵盖25个不同的属，代表环境物种，人类寄生虫，和机会人类病原体。在这里，我们专注于恢复一个几乎完整的基因组代表一种新的菌株的牙周病原体牙龈卟啉单胞菌（P. gingivalis JCVI SC001）使用单细胞组装工具SPAdes。单细胞基因组学正在成为捕获新基因组的公认方法，主要是在海洋和土壤环境中。在这里，我们第一次表明，它也使比较基因组分析的菌株变异的病原体从复杂的生物膜样品中捕获的医疗机构。
Although biofilms have been shown to be reservoirs of pathogens, our knowledge of the microbial diversity in biofilms within critical areas, such as health care facilities, is limited. Available methods for pathogen identification and strain typing have some inherent restrictions. In particular, culturing will yield only a fraction of the species present, PCR of virulence or marker genes is mainly focused on a handful of known species, and shotgun metagenomics is limited in the ability to detect strain variations. In this study, we present a single-cell genome sequencing approach to address these limitations and demonstrate it by specifically targeting bacterial cells within a complex biofilm from a hospital bathroom sink drain. A newly developed, automated platform was used to generate genomic DNA by the multiple displacement amplification (MDA) technique from hundreds of single cells in parallel. MDA reactions were screened and classified by 16S rRNA gene PCR sequence, which revealed a broad range of bacteria covering 25 different genera representing environmental species, human commensals, and opportunistic human pathogens. Here we focus on the recovery of a nearly complete genome representing a novel strain of the periodontal pathogen Porphyromonas gingivalis (P. gingivalis JCVI SC001) using the single-cell assembly tool SPAdes. Single-cell genomics is becoming an accepted method to capture novel genomes, primarily in the marine and soil environments. Here we show for the first time that it also enables comparative genomic analysis of strain variation in a pathogen captured from complex biofilm samples in a healthcare facility.
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影响因子：
4.2
作者：
Brunner J;Wittink FR;Jonker MJ;de Jong M;Breit TM;Laine ML;de Soet JJ;Crielaard W
通讯作者：
Crielaard W
影响因子：
56.9
作者：
Gill, Steven R.;Pop, Mihai;Nelson, Karen E.
通讯作者：
Nelson, Karen E.
DOI：
10.1073/pnas.0908446106
发表时间：
2009-09-22
影响因子：
11.1
作者：
Feazel, Leah M.;Baumgartner, Laura K.;Pace, Norman R.
通讯作者：
Pace, Norman R.
影响因子：
1.7
作者：
Bankevich, Anton;Nurk, Sergey;Pevzner, Pavel A.
通讯作者：
Pevzner, Pavel A.
影响因子：
3.7
作者：
Flores GE;Bates ST;Knights D;Lauber CL;Stombaugh J;Knight R;Fierer N
通讯作者：
Fierer N