Goyal Manisha, Javerliat Fabien, Palmieri Mattia, Mirande Caroline, van Wamel Willem, Tavakol Mehri, Verkaik Nelianne J, van Belkum Alex
Data Analytics Unit, bioMérieux, La Balme-les-Grottes, France.
Microbiology R&D, bioMérieux, La Balme-les-Grottes, France.
Front Microbiol. 2019 Jul 5;10:1525. doi: 10.3389/fmicb.2019.01525. eCollection 2019.
can colonize the human vestibulum nasi for many years. It is unknown whether and, how adapts to this ecological niche during colonization. We determined the short (1 and 3 months) and mid-term (36 months) genomic evolution of in natural carriers and artificially colonized volunteers. Eighty-five strains were collected from 6 natural carriers during 3 years and 6 artificially colonized volunteers during 1 month. Multi-locus sequence typing (MLST) and single nucleotide polymorphism (SNP) analysis based on whole-genome sequencing (WGS) were carried out. Mutation frequencies within resident bacterial populations over time were quantified using core genome SNP counts (comparing groups of genomes) and pairwise SNP divergence assessment (comparing two genomes from strains originating from one host and sharing identical MLST). SNP counts (within 1-3 months) in all naturally colonizing strains varied from 0 to 757 (median 4). These strains showed random and independent patterns of pairwise SNP divergence (0 to 44 SNPs, median 7). When the different core genome SNP counts over a period of 3 years were considered, the median SNP count was 4 (range 0-26). Host-specific pairwise SNP divergence for the same period ranged from 9 to 57 SNPs (median 20). During short term artificial colonization the mutation frequency was even lower (0-7 SNPs, median 2) and the pairwise SNP distances were 0 to 5 SNPs (median 2). Quantifying mutation frequencies is important for the longitudinal follow-up of epidemics of infections and outbreak management. Random pattern of pairwise SNP divergence between the strains isolated from single carriers suggested that the WGS of multiple colonies is necessary in this context. Over periods up to 3 years, maximum median core genome SNP counts and SNP divergence for the strains studied were 4 and 20 SNPs or lower. During artificial colonization, where median core genome SNP and pairwise SNP distance scores were 2, there is no early stage selection of different genotypes. Therefore, we suggest an epidemiological cut off value of 20 SNPs as a marker of strain identity during studies on nasal colonization and also outbreaks of infection.
可在人类鼻前庭定植多年。目前尚不清楚在定植过程中是否以及如何适应这一生态位。我们确定了自然携带者和人工定植志愿者中该菌短期（1个月和3个月）和中期（36个月）的基因组进化情况。在3年期间从6名自然携带者以及1个月期间从6名人工定植志愿者中收集了85株该菌。进行了多位点序列分型（MLST）和基于全基因组测序（WGS）的单核苷酸多态性（SNP）分析。使用核心基因组SNP计数（比较基因组组）和成对SNP差异评估（比较来自同一宿主且具有相同MLST的菌株的两个基因组）对常驻细菌群体随时间的突变频率进行了量化。所有自然定植菌株在1 - 3个月内的SNP计数从0到757不等（中位数为4）。这些菌株显示出成对SNP差异的随机且独立模式（0至44个SNP，中位数为7）。当考虑3年期间不同的核心基因组SNP计数时，中位数SNP计数为4（范围0 - 26）。同期宿主特异性成对SNP差异范围为9至57个SNP（中位数为20）。在短期人工定植期间，突变频率甚至更低（0 - 7个SNP，中位数为2），成对SNP距离为0至5个SNP（中位数为2）。量化突变频率对于感染流行的纵向随访和暴发管理很重要。从单个携带者分离的菌株之间成对SNP差异的随机模式表明，在此背景下对多个菌落进行WGS是必要的。在长达3年的时间里，所研究菌株的最大中位数核心基因组SNP计数和SNP差异分别为4和20个SNP或更低。在人工定植期间，核心基因组SNP和成对SNP距离得分的中位数为2，没有对不同基因型的早期选择。因此，我们建议在鼻腔定植研究以及感染暴发研究中，将20个SNP的流行病学截断值作为该菌菌株同一性的标志物。
