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The Epidome :
The Epidome : a species-specific approach to assess the population structure and heterogeneity of Staphylococcus epidermidis colonization and infection
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- Rendboe, Amalie Katrine (författare)
- Statens Serum Inst, Dept Bacteria Parasites & Fungi, Copenhagen, Denmark,Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
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- Johannesen, Thor Bech (författare)
- Statens Serum Inst, Dept Bacteria Parasites & Fungi, Copenhagen, Denmark,Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
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- Ingham, Anna Cäcilia (författare)
- Statens Serum Inst, Dept Bacteria Parasites & Fungi, Copenhagen, Denmark,Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
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- Månsson, Emeli (författare)
- Uppsala universitet,Centrum för klinisk forskning, Västerås,Örebro Univ, Fac Med & Hlth, Sch Med Sci, Örebro, Sweden,School of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden; Centre for Clinical Research, Hospital of Västmanland, Region Västmanland - Uppsala University, Västerås, Sweden
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- Iversen, Søren (författare)
- Statens Serum Inst, Dept Bacteria Parasites & Fungi, Copenhagen, Denmark,Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
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- Baig, Sharmin (författare)
- Statens Serum Inst, Dept Bacteria Parasites & Fungi, Copenhagen, Denmark,Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
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- Edslev, Sofie (författare)
- Statens Serum Inst, Dept Bacteria Parasites & Fungi, Copenhagen, Denmark,Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
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- Jensen, Jørgen Skov (författare)
- Statens Serum Inst, Dept Bacteria Parasites & Fungi, Copenhagen, Denmark,Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
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- Söderquist, Bo, 1955- (författare)
- Örebro universitet,Institutionen för medicinska vetenskaper,Örebro Univ, Fac Med & Hlth, Sch Med Sci, Örebro, Sweden
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- Andersen, Paal Skytt (författare)
- Statens Serum Inst, Dept Bacteria Parasites & Fungi, Copenhagen, Denmark,Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
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- Stegger, Marc, 1975- (författare)
- Örebro universitet,Institutionen för medicinska vetenskaper,Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark,Statens Serum Inst, Dept Bacteria Parasites & Fungi, Copenhagen, Denmark; Örebro Univ, Fac Med & Hlth, Sch Med Sci, Örebro, Sweden
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(creator_code:org_t)
- 2020-11-26
- 2020
- Engelska.
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Ingår i: BMC Microbiology. - : Springer Science and Business Media LLC. - 1471-2180. ; 20:1
- Relaterad länk:
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https://doi.org/10.1...
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https://uu.diva-port... (primary) (Raw object)
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https://bmcmicrobiol...
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https://urn.kb.se/re...
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https://doi.org/10.1...
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https://urn.kb.se/re...
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Abstract
Ämnesord
Stäng
- BackgroundAlthough 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.ResultsBased 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.ConclusionsThe 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.
Ämnesord
- NATURVETENSKAP -- Biologi -- Mikrobiologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Microbiology (hsv//eng)
- MEDICIN OCH HÄLSOVETENSKAP -- Medicinska och farmaceutiska grundvetenskaper -- Mikrobiologi inom det medicinska området (hsv//swe)
- MEDICAL AND HEALTH SCIENCES -- Basic Medicine -- Microbiology in the medical area (hsv//eng)
- NATURVETENSKAP -- Biologi -- Evolutionsbiologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Evolutionary Biology (hsv//eng)
Nyckelord
- Targeted sequencing
- Staphylococcus epidermidis
- Sequencing
- Population structure
- Heterogeneity
- Population dynamics
- Clonal lineages
- S
- epidermidis
- Amplicon sequence variant
- Species-specific classification
Publikations- och innehållstyp
- ref (ämneskategori)
- art (ämneskategori)
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Rendboe, Amalie ...
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Johannesen, Thor ...
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Ingham, Anna Cäc ...
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Månsson, Emeli
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Iversen, Søren
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Baig, Sharmin
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Edslev, Sofie
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Jensen, Jørgen S ...
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Söderquist, Bo, ...
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Andersen, Paal S ...
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Stegger, Marc, 1 ...
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- Om ämnet
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- NATURVETENSKAP
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NATURVETENSKAP
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och Biologi
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och Mikrobiologi
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- MEDICIN OCH HÄLSOVETENSKAP
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MEDICIN OCH HÄLS ...
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och Medicinska och f ...
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och Mikrobiologi ino ...
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- NATURVETENSKAP
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NATURVETENSKAP
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och Biologi
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och Evolutionsbiolog ...
- Artiklar i publikationen
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BMC Microbiology
- Av lärosätet
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Uppsala universitet
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Örebro universitet