The Epidome - a species-specific approach to assess the population structure and heterogeneity of Staphylococcus epidermidis colonization and infection

BMC Microbiology

article

Rendboe, Amalie Katrine¹  Andersen, Paal Skytt¹  Stegger, Marc¹  Johannesen, Thor Bech¹  Ingham, Anna Cäcilia¹  Månsson, Emeli²  Iversen, Søren¹  Baig, Sharmin¹  Edslev, Sofie¹  Jensen, Jørgen Skov¹  Söderquist, Bo² 

[1] Department of Bacteria, Statens Serum Institut;School of Medical Sciences, Faculty of Medicine and Health, Örebro University;Centre for Clinical Research, Hospital of Västmanland, Region Västmanland – Uppsala University

关键词: Targeted sequencing;    Staphylococcus epidermidis;    Sequencing;    Population structure;    Heterogeneity;    Population dynamics;    Clonal lineages;    S;    epidermidis;    Amplicon sequence variant;    Species-specific classification;   

DOI  :  10.1186/s12866-020-02041-w

学科分类：放射科、核医学、医学影像

来源: BioMed Central

【 摘 要 】

Although generally known as a human commensal, Staphylococcus epidermidis is also an opportunistic pathogen that can cause nosocomial infections related to foreign body materials and immunocompromized patients. Infections are often caused by multidrug-resistant (MDR) lineages that are difficult and costly to treat, and can have a major adverse impact on patients’ quality of life. Heterogeneity is a common phenomenon in both carriage and infection, but present methodology for detection of this is laborious or expensive. In this study, we present a culture-independent method, labelled Epidome, based on an amplicon sequencing-approach to deliver information beyond species level on primary samples and to elucidate clonality, population structure and temporal stability or niche selection of S. epidermidis communities. Based on an assessment of > 800 genes from the S. epidermidis core genome, we identified genes with variable regions, which in combination facilitated the differentiation of phylogenetic clusters observed in silico, and allowed classification down to lineage level. A duplex PCR, combined with an amplicon sequencing protocol, and a downstream analysis pipeline were designed to provide subspecies information from primary samples. Additionally, a probe-based qPCR was designed to provide valuable absolute abundance quantification of S. epidermidis. The approach was validated on isolates representing skin commensals and on genomic mock communities with a sensitivity of < 10 copies/μL. The method was furthermore applied to a sample set of primary skin and nasal samples, revealing a high degree of heterogeneity in the S. epidermidis populations. Additionally, the qPCR showed a high degree of variation in absolute abundance of S. epidermidis. The Epidome method is designed for use on primary samples to obtain important information on S. epidermidis abundance and diversity beyond species-level to answer questions regarding the emergence and dissemination of nosocomial lineages, investigating clonality of S. epidermidis communities, population dynamics, and niche selection. Our targeted-sequencing method allows rapid differentiation and identification of clinically important nosocomial lineages in low-biomass samples such as skin samples.

【 授权许可】

CC BY|CC0