The Epidome - a species-specific approach to assess the population structure and heterogeneity of Staphylococcus epidermidis colonization and infection
Abstract Background 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 tha...
Main Authors: | , , , , , , , , , , |
---|---|
Format: | Article |
Language: | English |
Published: |
BMC
2020-11-01
|
Series: | BMC Microbiology |
Subjects: | |
Online Access: | http://link.springer.com/article/10.1186/s12866-020-02041-w |
id |
doaj-fdac71208983400fa4d56041f6eec4a8 |
---|---|
record_format |
Article |
spelling |
doaj-fdac71208983400fa4d56041f6eec4a82020-11-26T12:51:04ZengBMCBMC Microbiology1471-21802020-11-0120111310.1186/s12866-020-02041-wThe Epidome - a species-specific approach to assess the population structure and heterogeneity of Staphylococcus epidermidis colonization and infectionAmalie Katrine Rendboe0Thor Bech Johannesen1Anna Cäcilia Ingham2Emeli Månsson3Søren Iversen4Sharmin Baig5Sofie Edslev6Jørgen Skov Jensen7Bo Söderquist8Paal Skytt Andersen9Marc Stegger10Department of Bacteria, Parasites and Fungi, Statens Serum InstitutDepartment of Bacteria, Parasites and Fungi, Statens Serum InstitutDepartment of Bacteria, Parasites and Fungi, Statens Serum InstitutSchool of Medical Sciences, Faculty of Medicine and Health, Örebro UniversityDepartment of Bacteria, Parasites and Fungi, Statens Serum InstitutDepartment of Bacteria, Parasites and Fungi, Statens Serum InstitutDepartment of Bacteria, Parasites and Fungi, Statens Serum InstitutDepartment of Bacteria, Parasites and Fungi, Statens Serum InstitutSchool of Medical Sciences, Faculty of Medicine and Health, Örebro UniversityDepartment of Bacteria, Parasites and Fungi, Statens Serum InstitutDepartment of Bacteria, Parasites and Fungi, Statens Serum InstitutAbstract Background 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. Results 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. Conclusions 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.http://link.springer.com/article/10.1186/s12866-020-02041-wTargeted sequencingStaphylococcus epidermidisSequencingPopulation structureHeterogeneityPopulation dynamics |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Amalie Katrine Rendboe Thor Bech Johannesen Anna Cäcilia Ingham Emeli Månsson Søren Iversen Sharmin Baig Sofie Edslev Jørgen Skov Jensen Bo Söderquist Paal Skytt Andersen Marc Stegger |
spellingShingle |
Amalie Katrine Rendboe Thor Bech Johannesen Anna Cäcilia Ingham Emeli Månsson Søren Iversen Sharmin Baig Sofie Edslev Jørgen Skov Jensen Bo Söderquist Paal Skytt Andersen Marc Stegger The Epidome - a species-specific approach to assess the population structure and heterogeneity of Staphylococcus epidermidis colonization and infection BMC Microbiology Targeted sequencing Staphylococcus epidermidis Sequencing Population structure Heterogeneity Population dynamics |
author_facet |
Amalie Katrine Rendboe Thor Bech Johannesen Anna Cäcilia Ingham Emeli Månsson Søren Iversen Sharmin Baig Sofie Edslev Jørgen Skov Jensen Bo Söderquist Paal Skytt Andersen Marc Stegger |
author_sort |
Amalie Katrine Rendboe |
title |
The Epidome - a species-specific approach to assess the population structure and heterogeneity of Staphylococcus epidermidis colonization and infection |
title_short |
The Epidome - a species-specific approach to assess the population structure and heterogeneity of Staphylococcus epidermidis colonization and infection |
title_full |
The Epidome - a species-specific approach to assess the population structure and heterogeneity of Staphylococcus epidermidis colonization and infection |
title_fullStr |
The Epidome - a species-specific approach to assess the population structure and heterogeneity of Staphylococcus epidermidis colonization and infection |
title_full_unstemmed |
The Epidome - a species-specific approach to assess the population structure and heterogeneity of Staphylococcus epidermidis colonization and infection |
title_sort |
epidome - a species-specific approach to assess the population structure and heterogeneity of staphylococcus epidermidis colonization and infection |
publisher |
BMC |
series |
BMC Microbiology |
issn |
1471-2180 |
publishDate |
2020-11-01 |
description |
Abstract Background 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. Results 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. Conclusions 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. |
topic |
Targeted sequencing Staphylococcus epidermidis Sequencing Population structure Heterogeneity Population dynamics |
url |
http://link.springer.com/article/10.1186/s12866-020-02041-w |
work_keys_str_mv |
AT amaliekatrinerendboe theepidomeaspeciesspecificapproachtoassessthepopulationstructureandheterogeneityofstaphylococcusepidermidiscolonizationandinfection AT thorbechjohannesen theepidomeaspeciesspecificapproachtoassessthepopulationstructureandheterogeneityofstaphylococcusepidermidiscolonizationandinfection AT annacaciliaingham theepidomeaspeciesspecificapproachtoassessthepopulationstructureandheterogeneityofstaphylococcusepidermidiscolonizationandinfection AT emelimansson theepidomeaspeciesspecificapproachtoassessthepopulationstructureandheterogeneityofstaphylococcusepidermidiscolonizationandinfection AT søreniversen theepidomeaspeciesspecificapproachtoassessthepopulationstructureandheterogeneityofstaphylococcusepidermidiscolonizationandinfection AT sharminbaig theepidomeaspeciesspecificapproachtoassessthepopulationstructureandheterogeneityofstaphylococcusepidermidiscolonizationandinfection AT sofieedslev theepidomeaspeciesspecificapproachtoassessthepopulationstructureandheterogeneityofstaphylococcusepidermidiscolonizationandinfection AT jørgenskovjensen theepidomeaspeciesspecificapproachtoassessthepopulationstructureandheterogeneityofstaphylococcusepidermidiscolonizationandinfection AT bosoderquist theepidomeaspeciesspecificapproachtoassessthepopulationstructureandheterogeneityofstaphylococcusepidermidiscolonizationandinfection AT paalskyttandersen theepidomeaspeciesspecificapproachtoassessthepopulationstructureandheterogeneityofstaphylococcusepidermidiscolonizationandinfection AT marcstegger theepidomeaspeciesspecificapproachtoassessthepopulationstructureandheterogeneityofstaphylococcusepidermidiscolonizationandinfection AT amaliekatrinerendboe epidomeaspeciesspecificapproachtoassessthepopulationstructureandheterogeneityofstaphylococcusepidermidiscolonizationandinfection AT thorbechjohannesen epidomeaspeciesspecificapproachtoassessthepopulationstructureandheterogeneityofstaphylococcusepidermidiscolonizationandinfection AT annacaciliaingham epidomeaspeciesspecificapproachtoassessthepopulationstructureandheterogeneityofstaphylococcusepidermidiscolonizationandinfection AT emelimansson epidomeaspeciesspecificapproachtoassessthepopulationstructureandheterogeneityofstaphylococcusepidermidiscolonizationandinfection AT søreniversen epidomeaspeciesspecificapproachtoassessthepopulationstructureandheterogeneityofstaphylococcusepidermidiscolonizationandinfection AT sharminbaig epidomeaspeciesspecificapproachtoassessthepopulationstructureandheterogeneityofstaphylococcusepidermidiscolonizationandinfection AT sofieedslev epidomeaspeciesspecificapproachtoassessthepopulationstructureandheterogeneityofstaphylococcusepidermidiscolonizationandinfection AT jørgenskovjensen epidomeaspeciesspecificapproachtoassessthepopulationstructureandheterogeneityofstaphylococcusepidermidiscolonizationandinfection AT bosoderquist epidomeaspeciesspecificapproachtoassessthepopulationstructureandheterogeneityofstaphylococcusepidermidiscolonizationandinfection AT paalskyttandersen epidomeaspeciesspecificapproachtoassessthepopulationstructureandheterogeneityofstaphylococcusepidermidiscolonizationandinfection AT marcstegger epidomeaspeciesspecificapproachtoassessthepopulationstructureandheterogeneityofstaphylococcusepidermidiscolonizationandinfection |
_version_ |
1724414621747511296 |