Strain-level resolution and pneumococcal carriage dynamics by single-molecule real-time (SMRT) sequencing of the plyNCR marker: a longitudinal study in Swiss infants
Abstract Background Pneumococcal carriage has often been studied from a serotype perspective; however, little is known about the strain-specific carriage and inter-strain interactions. Here, we examined the strain-level carriage and co-colonization dynamics of Streptococcus pneumoniae in a Swiss bir...
| Main Authors: | , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2022-09-01
|
| Series: | Microbiome |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s40168-022-01344-6 |
| _version_ | 1811265214017961984 |
|---|---|
| author | Oluwaseun Rume-Abiola Oyewole Philipp Latzin Silvio D. Brugger Markus Hilty |
| author_facet | Oluwaseun Rume-Abiola Oyewole Philipp Latzin Silvio D. Brugger Markus Hilty |
| author_sort | Oluwaseun Rume-Abiola Oyewole |
| collection | DOAJ |
| description | Abstract Background Pneumococcal carriage has often been studied from a serotype perspective; however, little is known about the strain-specific carriage and inter-strain interactions. Here, we examined the strain-level carriage and co-colonization dynamics of Streptococcus pneumoniae in a Swiss birth cohort by PacBio single-molecule real-time (SMRT) sequencing of the plyNCR marker. Methods A total of 872 nasal swab (NS) samples were included from 47 healthy infants during the first year of life. Pneumococcal carriage was determined based on the quantitative real-time polymerase chain reaction (qPCR) targeting the lytA gene. The plyNCR marker was amplified from 214 samples having lytA-based carriage for pneumococcal strain resolution. Amplicons were sequenced using SMRT technology, and sequences were analyzed with the DADA2 pipeline. In addition, pneumococcal serotypes were determined using conventional, multiplex PCR (cPCR). Results PCR-based plyNCR amplification demonstrated a 94.2% sensitivity and 100% specificity for Streptococcus pneumoniae if compared to lytA qPCR. The overall carriage prevalence was 63.8%, and pneumococcal co-colonization (≥ 2 plyNCR amplicon sequence variants (ASVs)) was detected in 38/213 (17.8%) sequenced samples with the relative proportion of the least abundant strain(s) ranging from 1.1 to 48.8% (median, 17.2%; IQR, 5.8–33.4%). The median age to first acquisition was 147 days, and having ≥ 2 siblings increased the risk of acquisition. Conclusion The plyNCR amplicon sequencing is species-specific and enables pneumococcal strain resolution. We therefore recommend its application for longitudinal strain-level carriage studies of Streptococcus pneumoniae. Video Abstract |
| first_indexed | 2024-04-12T20:19:38Z |
| format | Article |
| id | doaj.art-bd31d554bae042e6bc9836f0258df617 |
| institution | Directory Open Access Journal |
| issn | 2049-2618 |
| language | English |
| last_indexed | 2024-04-12T20:19:38Z |
| publishDate | 2022-09-01 |
| publisher | BMC |
| record_format | Article |
| series | Microbiome |
| spelling | doaj.art-bd31d554bae042e6bc9836f0258df6172022-12-22T03:18:02ZengBMCMicrobiome2049-26182022-09-0110111510.1186/s40168-022-01344-6Strain-level resolution and pneumococcal carriage dynamics by single-molecule real-time (SMRT) sequencing of the plyNCR marker: a longitudinal study in Swiss infantsOluwaseun Rume-Abiola Oyewole0Philipp Latzin1Silvio D. Brugger2Markus Hilty3Institute for Infectious Diseases, University of BernDivision of Respiratory Medicine, Department of Pediatrics, Inselspital, University of BernDepartment of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of ZurichInstitute for Infectious Diseases, University of BernAbstract Background Pneumococcal carriage has often been studied from a serotype perspective; however, little is known about the strain-specific carriage and inter-strain interactions. Here, we examined the strain-level carriage and co-colonization dynamics of Streptococcus pneumoniae in a Swiss birth cohort by PacBio single-molecule real-time (SMRT) sequencing of the plyNCR marker. Methods A total of 872 nasal swab (NS) samples were included from 47 healthy infants during the first year of life. Pneumococcal carriage was determined based on the quantitative real-time polymerase chain reaction (qPCR) targeting the lytA gene. The plyNCR marker was amplified from 214 samples having lytA-based carriage for pneumococcal strain resolution. Amplicons were sequenced using SMRT technology, and sequences were analyzed with the DADA2 pipeline. In addition, pneumococcal serotypes were determined using conventional, multiplex PCR (cPCR). Results PCR-based plyNCR amplification demonstrated a 94.2% sensitivity and 100% specificity for Streptococcus pneumoniae if compared to lytA qPCR. The overall carriage prevalence was 63.8%, and pneumococcal co-colonization (≥ 2 plyNCR amplicon sequence variants (ASVs)) was detected in 38/213 (17.8%) sequenced samples with the relative proportion of the least abundant strain(s) ranging from 1.1 to 48.8% (median, 17.2%; IQR, 5.8–33.4%). The median age to first acquisition was 147 days, and having ≥ 2 siblings increased the risk of acquisition. Conclusion The plyNCR amplicon sequencing is species-specific and enables pneumococcal strain resolution. We therefore recommend its application for longitudinal strain-level carriage studies of Streptococcus pneumoniae. Video Abstracthttps://doi.org/10.1186/s40168-022-01344-6Respiratory microbiomePacBio single-molecule real-time (SMRT) sequencingDADA2Co-colonizationStreptococcus pneumoniaeCarriage duration |
| spellingShingle | Oluwaseun Rume-Abiola Oyewole Philipp Latzin Silvio D. Brugger Markus Hilty Strain-level resolution and pneumococcal carriage dynamics by single-molecule real-time (SMRT) sequencing of the plyNCR marker: a longitudinal study in Swiss infants Microbiome Respiratory microbiome PacBio single-molecule real-time (SMRT) sequencing DADA2 Co-colonization Streptococcus pneumoniae Carriage duration |
| title | Strain-level resolution and pneumococcal carriage dynamics by single-molecule real-time (SMRT) sequencing of the plyNCR marker: a longitudinal study in Swiss infants |
| title_full | Strain-level resolution and pneumococcal carriage dynamics by single-molecule real-time (SMRT) sequencing of the plyNCR marker: a longitudinal study in Swiss infants |
| title_fullStr | Strain-level resolution and pneumococcal carriage dynamics by single-molecule real-time (SMRT) sequencing of the plyNCR marker: a longitudinal study in Swiss infants |
| title_full_unstemmed | Strain-level resolution and pneumococcal carriage dynamics by single-molecule real-time (SMRT) sequencing of the plyNCR marker: a longitudinal study in Swiss infants |
| title_short | Strain-level resolution and pneumococcal carriage dynamics by single-molecule real-time (SMRT) sequencing of the plyNCR marker: a longitudinal study in Swiss infants |
| title_sort | strain level resolution and pneumococcal carriage dynamics by single molecule real time smrt sequencing of the plyncr marker a longitudinal study in swiss infants |
| topic | Respiratory microbiome PacBio single-molecule real-time (SMRT) sequencing DADA2 Co-colonization Streptococcus pneumoniae Carriage duration |
| url | https://doi.org/10.1186/s40168-022-01344-6 |
| work_keys_str_mv | AT oluwaseunrumeabiolaoyewole strainlevelresolutionandpneumococcalcarriagedynamicsbysinglemoleculerealtimesmrtsequencingoftheplyncrmarkeralongitudinalstudyinswissinfants AT philipplatzin strainlevelresolutionandpneumococcalcarriagedynamicsbysinglemoleculerealtimesmrtsequencingoftheplyncrmarkeralongitudinalstudyinswissinfants AT silviodbrugger strainlevelresolutionandpneumococcalcarriagedynamicsbysinglemoleculerealtimesmrtsequencingoftheplyncrmarkeralongitudinalstudyinswissinfants AT markushilty strainlevelresolutionandpneumococcalcarriagedynamicsbysinglemoleculerealtimesmrtsequencingoftheplyncrmarkeralongitudinalstudyinswissinfants |