Comparison of genomic diversity between single and pooled Staphylococcus aureus colonies isolated from human colonisation cultures.
Comparison of genomic diversity between single and pooled Staphylococcus aureus colonies isolated from human colonisation cultures.
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从人类定植培养物中分离出的单个金黄色葡萄球菌菌落和混合金黄色葡萄球菌菌落之间的基因组多样性的比较。
DOI：
10.1101/2023.06.14.544959
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发表时间：
2023
期刊：
影响因子：
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通讯作者：
David,MichaelZ
中科院分区：
文献类型：
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作者：
Raghuram,Vishnu;Gunoskey,JessicaJ;Hofstetter,KatrinaS;Jacko,NatasiaF;Shumaker,MargotJ;Hu,Yi-Juan;Read,TimothyD;David,MichaelZ
对感染或定殖宿主内的细菌群体进行取样的最常见方法是对从培养板获得的单个菌落的基因组进行测序。然而，人们认识到，这种方法不能捕捉到种群的遗传多样性。对几个菌落的混合物进行测序（pool-seq）是检测群体异质性的更好方法，但由于不同类型的异质性，如克隆内多态性，多菌株混合物，多物种混合物和污染，分析起来更加复杂。在这里，我们在一组2286个金黄色葡萄球菌培养样本上比较了8个单菌落分离株（singles）和pool-seq，以确定可以区分纯样本、经历克隆内变异的样本和混合菌株样本的特征。这些样本是通过对85名参与者的3个身体部位进行为期一年的季度擦拭而获得的，这些参与者最初表现为甲氧西林耐药。金黄色皮肤软组织感染（SSTI）。我们比较了每个池中的参数，如序列质量，污染，等位基因频率，核苷酸多样性和泛基因组多样性与相应的单打。比较来自同一培养板的单个样本，我们发现18%的样本集合包含多个多位点序列类型（MLST或ST）的混合物。我们发现，仅pool-seq数据就可以预测多ST群体的存在，准确率为95%。我们还表明，pool-seq可以用来估计种群中克隆内多态位点的数量。此外，我们发现，该池可能包含临床相关的基因，如抗生素耐药性标记，可能会错过时，只检查单打。这些结果突出了分析从临床培养物而不是单个菌落获得的总群体的基因组序列的潜在优势。
The most common approach to sampling the bacterial populations within an infected or colonized host is to sequence genomes from a single colony obtained from a culture plate. However, it is recognized that this method does not capture the genetic diversity in the population. Sequencing a mixture of several colonies (pool-seq) is a better approach to detect population heterogeneity, but it is more complex to analyse due to different types of heterogeneity, such as within-clone polymorphisms, multi-strain mixtures, multi-species mixtures and contamination. Here, we compared 8 single-colony isolates (singles) and pool-seq on a set of 2286Staphylococcus aureusculture samples to identify features that can distinguish pure samples, samples undergoing intraclonal variation and mixed strain samples. The samples were obtained by swabbing 3 body sites on 85 human participants quarterly for a year, who initially presented with a methicillin-resistantS. aureusskin and soft-tissue infection (SSTI). We compared parameters such as sequence quality, contamination, allele frequency, nucleotide diversity and pangenome diversity in each pool to those for the corresponding singles. Comparing singles from the same culture plate, we found that 18% of sample collections contained mixtures of multiple multilocus sequence types (MLSTs or STs). We showed that pool-seq data alone could predict the presence of multi-ST populations with 95% accuracy. We also showed that pool-seq could be used to estimate the number of intra-clonal polymorphic sites in the population. Additionally, we found that the pool may contain clinically relevant genes such as antimicrobial resistance markers that may be missed when only examining singles. These results highlight the potential advantage of analysing genome sequences of total populations obtained from clinical cultures rather than single colonies.