Development and implementation of a core genome multilocus sequence typing scheme for Haemophilus influenzae.

IF 4 2区 生物学 Q1 GENETICS & HEREDITY
Made Ananda Krisna, Keith A Jolley, William Monteith, Alexandra Boubour, Raph L Hamers, Angela B Brueggemann, Odile B Harrison, Martin C J Maiden
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引用次数: 0

Abstract

Haemophilus influenzae is part of the human nasopharyngeal microbiota and a pathogen causing invasive disease. The extensive genetic diversity observed in H. influenzae necessitates discriminatory analytical approaches to evaluate its population structure. This study developed a core genome multilocus sequence typing (cgMLST) scheme for H. influenzae using pangenome analysis tools and validated the cgMLST scheme using datasets consisting of complete reference genomes (N = 14) and high-quality draft H. influenzae genomes (N = 2297). The draft genome dataset was divided into a development dataset (N = 921) and a validation dataset (N = 1376). The development dataset was used to identify potential core genes, and the validation dataset was used to refine the final core gene list to ensure the reliability of the proposed cgMLST scheme. Functional classifications were made for all the resulting core genes. Phylogenetic analyses were performed using both allelic profiles and nucleotide sequence alignments of the core genome to test congruence, as assessed by Spearman's correlation and ordinary least square linear regression tests. Preliminary analyses using the development dataset identified 1067 core genes, which were refined to 1037 with the validation dataset. More than 70% of core genes were predicted to encode proteins essential for metabolism or genetic information processing. Phylogenetic and statistical analyses indicated that the core genome allelic profile accurately represented phylogenetic relatedness among the isolates (R 2 = 0.945). We used this cgMLST scheme to define a high-resolution population structure for H. influenzae, which enhances the genomic analysis of this clinically relevant human pathogen.

开发和实施流感嗜血杆菌核心基因组多焦点序列分型方案。
流感嗜血杆菌是人类鼻咽部微生物群的一部分,也是导致侵袭性疾病的病原体。流感嗜血杆菌具有广泛的遗传多样性,因此有必要采用鉴别分析方法来评估其种群结构。本研究利用泛基因组分析工具为流感嗜血杆菌开发了核心基因组多焦点序列分型(cgMLST)方案,并利用由完整参考基因组(N = 14)和高质量流感嗜血杆菌基因组草案(N = 2297)组成的数据集验证了cgMLST方案。基因组草案数据集分为开发数据集(N = 921)和验证数据集(N = 1376)。开发数据集用于确定潜在的核心基因,验证数据集用于完善最终的核心基因列表,以确保拟议的 cgMLST 方案的可靠性。对所有产生的核心基因进行了功能分类。利用等位基因图谱和核心基因组的核苷酸序列比对进行了系统发育分析,通过斯皮尔曼相关性和普通最小二乘法线性回归测试来检验一致性。使用开发数据集进行的初步分析确定了 1067 个核心基因,使用验证数据集将其细化为 1037 个。据预测,70%以上的核心基因编码新陈代谢或遗传信息处理所必需的蛋白质。系统发育和统计分析表明,核心基因组等位基因图谱准确地代表了分离株之间的系统发育亲缘关系(R 2 = 0.945)。我们利用这种 cgMLST 方案确定了流感嗜血杆菌的高分辨率种群结构,从而加强了对这种与临床相关的人类病原体的基因组分析。
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来源期刊
Microbial Genomics
Microbial Genomics Medicine-Epidemiology
CiteScore
6.60
自引率
2.60%
发文量
153
审稿时长
12 weeks
期刊介绍: Microbial Genomics (MGen) is a fully open access, mandatory open data and peer-reviewed journal publishing high-profile original research on archaea, bacteria, microbial eukaryotes and viruses.
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