PneumoKITy: A fast, flexible, specific, and sensitive tool for Streptococcus pneumoniae serotype screening and mixed serotype detection from genome sequence data

Carmen L. Sheppard; Sam Manna; Natalie Groves; David J. Litt; Zahin Amin-Chowdhury; Marta Bertran; Shamez Ladhani; Catherine Satzke; Norman K. Fry

doi:10.1099/mgen.0.000904

PneumoKITy: A fast, flexible, specific, and sensitive tool for Streptococcus pneumoniae serotype screening and mixed serotype detection from genome sequence data

Carmen L. Sheppard, Sam Manna, Natalie Groves, David J. Litt, Zahin Amin-Chowdhury, Marta Bertran, Shamez Ladhani, Catherine Satzke, Norman K. Fry^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

2 Citations (Scopus)

Abstract

Determination of serotypes of Streptococcus pneumoniae is essential for monitoring current vaccine programmes. Since October 2017, pneumococcal serotypes in England have been derived from whole genome sequencing (WGS) data using our bioinformatic tool PneumoCaT. That tool was designed for serotype determination from pure cultures in a reference laboratory. To help determine multiple serotypes in pneumococcal carriage samples, we developed a new software tool named PneumoK-ITy (Pneumococcal K-mer Integrated Typing) that uses the powerful Mash k-mer screening method for pneumococcal serotyp-ing. Mash k-mer screening is more sequence specific and much faster than the mapping method used in PneumoCaT and can determine 54 (58.1 %) of the 93 serotypes in the SSI Diagnostica phenotypical serotyping scheme to type level with the remain-der called to serogroup or subgroup level (e.g., 11A/D). PneumoKITy can be run on both FastQ and assembly input, requiring up to 11× less memory and running up to 29× faster than the current version of PneumoCaT (1.2.1) on FastQ files. PneumoK-ITy can be used as a rapid, flexible serotype screening method which adds sensitive detection of mixed serotypes, e.g., for nasopharyngeal carriage studies where the presence of multiple serotypes is common. PneumoKITy’s ability to function from assembly file, for pure culture serotype detection, increases its speed. This speed potentially enables the software to be run using low infrastructure overhead via web-based platforms. PneumoKITy could be used as a fast initial screening method with other tools used for those serotypes that could not be fully determined to type level if necessary. PneumoKITy was found to be highly accurate and sensitive when run on a panel of FastQ files derived from mixed cultures with all serotypes in 47/51 (92.2 %) of samples being accurately detected. PneumoKITy was also able to accurately estimate the relative abundance of serotypes in the same sample. Estimates being within a mean relative abundance of 1.5 % of the expected abundance in mixtures with known concentrations. PneumoKITy was able to detect minor serotypes with expected abundance of 1 % in the known mixture serotypes. PneumoKITy is a rapid, flexible tool with wide-ranging applications outside of the pure-culture, reference laboratory serotyping remit of PneumoCaT.

Original language	English
Article number	000904
Journal	Microbial Genomics
Volume	8
Issue number	12
DOIs	https://doi.org/10.1099/mgen.0.000904
Publication status	Published - 2022

Bibliographical note

Funding Information:
Carmen Sheppard – recently joined a commercial company specialising in development of genome analysis platforms; however, this work was done prior to this change in affiliation. Public Health England (PHE), now the UK Health Security Agency (UKHSA) Immunisation and Vaccine Preventable Diseases Division provides vaccine manufacturers with post-marketing surveillance reports, which Marketing Authorisation Holders are required to submit to the UK Licensing authority in compliance with their Risk Management Strategy. A cost recovery charge is made for these reports. Sam Manna – None. Natalie Groves – Public Health England (PHE), now the UK Health Security Agency (UKHSA) Immunisation and Vaccine Preventable Diseases Division provides vaccine manufacturers with post-marketing surveillance reports, which Marketing Authorisation Holders are required to submit to the UK Licensing authority in compliance with their Risk Management Strategy. A cost recovery charge is made for these reports. David J. Litt – Public Health England (PHE), now the UK Health Security Agency (UKHSA) Immunisation and Vaccine Preventable Diseases Division provides vaccine manufacturers with post-marketing surveillance reports, which Marketing Authorisation Holders are required to submit to the UK Licensing authority in compliance with their Risk Management Strategy. A cost recovery charge is made for these reports. Zahin Amin-Chowdhury – Public Health England (PHE), now the UK Health Security Agency (UKHSA) Immunisation and Vaccine Preventable Diseases Division provides vaccine manufacturers with post-marketing surveillance reports, which Marketing Authorisation Holders are required to submit to the UK Licensing authority in compliance with their Risk Management Strategy. A cost recovery charge is made for these reports. Marta Bertran – Public Health England (PHE), now the UK Health Security Agency (UKHSA) Immunisation and Vaccine Preventable Diseases Division provides vaccine manufacturers with post-marketing surveillance reports, which Marketing Authorisation Holders are required to submit to the UK Licensing authority in compliance with their Risk Management Strategy. A cost recovery charge is made for these reports. Shamez Ladhani – Public Health England (PHE), now the UK Health Security Agency (UKHSA) Immunisation and Vaccine Preventable Diseases Division provides vaccine manufacturers with post-marketing surveillance reports, which Marketing Authorisation Holders are required to submit to the UK Licensing authority in compliance with their Risk Management Strategy. A cost recovery charge is made for these reports. Catherine Satzke – Lead investigator on a Merck Investigator Studies ProgramProgramme grant funded by MSD on pneumococcal serotype epidemiology. Investigator on a clinical research collaboration on PCV vaccination in Mongolia. Norman K. Fry – Public Health England (PHE), now the UK Health Security Agency (UKHSA) Immunisation and Vaccine Preventable Diseases Division provides vaccine manufacturers with post-marketing surveillance reports, which Marketing Authorisation Holders are required to submit to the UK Licensing authority in compliance with their Risk Management Strategy. A cost recovery charge is made for these reports. Dr NK Fry and his team conduct contract research for pharmaceutical industries on behalf of UKHSA (formerly PHE). No personal remuneration is received.

Publisher Copyright:
© 2022, Microbiology Society. All rights reserved.

Keywords

Pneumococcus
bioinformatics
carriage
colonisation
detection
epidemiology
serotyping
software

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

Access to Document

10.1099/mgen.0.000904

Cite this

Sheppard, C. L., Manna, S., Groves, N., Litt, D. J., Amin-Chowdhury, Z., Bertran, M., Ladhani, S., Satzke, C., & Fry, N. K. (2022). PneumoKITy: A fast, flexible, specific, and sensitive tool for Streptococcus pneumoniae serotype screening and mixed serotype detection from genome sequence data. Microbial Genomics, 8(12), Article 000904. https://doi.org/10.1099/mgen.0.000904

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title = "PneumoKITy: A fast, flexible, specific, and sensitive tool for Streptococcus pneumoniae serotype screening and mixed serotype detection from genome sequence data",

abstract = "Determination of serotypes of Streptococcus pneumoniae is essential for monitoring current vaccine programmes. Since October 2017, pneumococcal serotypes in England have been derived from whole genome sequencing (WGS) data using our bioinformatic tool PneumoCaT. That tool was designed for serotype determination from pure cultures in a reference laboratory. To help determine multiple serotypes in pneumococcal carriage samples, we developed a new software tool named PneumoK-ITy (Pneumococcal K-mer Integrated Typing) that uses the powerful Mash k-mer screening method for pneumococcal serotyp-ing. Mash k-mer screening is more sequence specific and much faster than the mapping method used in PneumoCaT and can determine 54 (58.1 %) of the 93 serotypes in the SSI Diagnostica phenotypical serotyping scheme to type level with the remain-der called to serogroup or subgroup level (e.g., 11A/D). PneumoKITy can be run on both FastQ and assembly input, requiring up to 11× less memory and running up to 29× faster than the current version of PneumoCaT (1.2.1) on FastQ files. PneumoK-ITy can be used as a rapid, flexible serotype screening method which adds sensitive detection of mixed serotypes, e.g., for nasopharyngeal carriage studies where the presence of multiple serotypes is common. PneumoKITy{\textquoteright}s ability to function from assembly file, for pure culture serotype detection, increases its speed. This speed potentially enables the software to be run using low infrastructure overhead via web-based platforms. PneumoKITy could be used as a fast initial screening method with other tools used for those serotypes that could not be fully determined to type level if necessary. PneumoKITy was found to be highly accurate and sensitive when run on a panel of FastQ files derived from mixed cultures with all serotypes in 47/51 (92.2 %) of samples being accurately detected. PneumoKITy was also able to accurately estimate the relative abundance of serotypes in the same sample. Estimates being within a mean relative abundance of 1.5 % of the expected abundance in mixtures with known concentrations. PneumoKITy was able to detect minor serotypes with expected abundance of 1 % in the known mixture serotypes. PneumoKITy is a rapid, flexible tool with wide-ranging applications outside of the pure-culture, reference laboratory serotyping remit of PneumoCaT.",

keywords = "Pneumococcus, bioinformatics, carriage, colonisation, detection, epidemiology, serotyping, software",

author = "Sheppard, {Carmen L.} and Sam Manna and Natalie Groves and Litt, {David J.} and Zahin Amin-Chowdhury and Marta Bertran and Shamez Ladhani and Catherine Satzke and Fry, {Norman K.}",

note = "Funding Information: Carmen Sheppard – recently joined a commercial company specialising in development of genome analysis platforms; however, this work was done prior to this change in affiliation. Public Health England (PHE), now the UK Health Security Agency (UKHSA) Immunisation and Vaccine Preventable Diseases Division provides vaccine manufacturers with post-marketing surveillance reports, which Marketing Authorisation Holders are required to submit to the UK Licensing authority in compliance with their Risk Management Strategy. A cost recovery charge is made for these reports. Sam Manna – None. Natalie Groves – Public Health England (PHE), now the UK Health Security Agency (UKHSA) Immunisation and Vaccine Preventable Diseases Division provides vaccine manufacturers with post-marketing surveillance reports, which Marketing Authorisation Holders are required to submit to the UK Licensing authority in compliance with their Risk Management Strategy. A cost recovery charge is made for these reports. David J. Litt – Public Health England (PHE), now the UK Health Security Agency (UKHSA) Immunisation and Vaccine Preventable Diseases Division provides vaccine manufacturers with post-marketing surveillance reports, which Marketing Authorisation Holders are required to submit to the UK Licensing authority in compliance with their Risk Management Strategy. A cost recovery charge is made for these reports. Zahin Amin-Chowdhury – Public Health England (PHE), now the UK Health Security Agency (UKHSA) Immunisation and Vaccine Preventable Diseases Division provides vaccine manufacturers with post-marketing surveillance reports, which Marketing Authorisation Holders are required to submit to the UK Licensing authority in compliance with their Risk Management Strategy. A cost recovery charge is made for these reports. Marta Bertran – Public Health England (PHE), now the UK Health Security Agency (UKHSA) Immunisation and Vaccine Preventable Diseases Division provides vaccine manufacturers with post-marketing surveillance reports, which Marketing Authorisation Holders are required to submit to the UK Licensing authority in compliance with their Risk Management Strategy. A cost recovery charge is made for these reports. Shamez Ladhani – Public Health England (PHE), now the UK Health Security Agency (UKHSA) Immunisation and Vaccine Preventable Diseases Division provides vaccine manufacturers with post-marketing surveillance reports, which Marketing Authorisation Holders are required to submit to the UK Licensing authority in compliance with their Risk Management Strategy. A cost recovery charge is made for these reports. Catherine Satzke – Lead investigator on a Merck Investigator Studies ProgramProgramme grant funded by MSD on pneumococcal serotype epidemiology. Investigator on a clinical research collaboration on PCV vaccination in Mongolia. Norman K. Fry – Public Health England (PHE), now the UK Health Security Agency (UKHSA) Immunisation and Vaccine Preventable Diseases Division provides vaccine manufacturers with post-marketing surveillance reports, which Marketing Authorisation Holders are required to submit to the UK Licensing authority in compliance with their Risk Management Strategy. A cost recovery charge is made for these reports. Dr NK Fry and his team conduct contract research for pharmaceutical industries on behalf of UKHSA (formerly PHE). No personal remuneration is received. Publisher Copyright: {\textcopyright} 2022, Microbiology Society. All rights reserved.",

year = "2022",

doi = "10.1099/mgen.0.000904",

language = "English",

volume = "8",

journal = "Microbial Genomics",

issn = "2057-5858",

publisher = "Microbiology Society",

number = "12",

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T2 - A fast, flexible, specific, and sensitive tool for Streptococcus pneumoniae serotype screening and mixed serotype detection from genome sequence data

AU - Sheppard, Carmen L.

AU - Manna, Sam

AU - Groves, Natalie

AU - Litt, David J.

AU - Amin-Chowdhury, Zahin

AU - Bertran, Marta

AU - Ladhani, Shamez

AU - Satzke, Catherine

AU - Fry, Norman K.

N1 - Funding Information: Carmen Sheppard – recently joined a commercial company specialising in development of genome analysis platforms; however, this work was done prior to this change in affiliation. Public Health England (PHE), now the UK Health Security Agency (UKHSA) Immunisation and Vaccine Preventable Diseases Division provides vaccine manufacturers with post-marketing surveillance reports, which Marketing Authorisation Holders are required to submit to the UK Licensing authority in compliance with their Risk Management Strategy. A cost recovery charge is made for these reports. Sam Manna – None. Natalie Groves – Public Health England (PHE), now the UK Health Security Agency (UKHSA) Immunisation and Vaccine Preventable Diseases Division provides vaccine manufacturers with post-marketing surveillance reports, which Marketing Authorisation Holders are required to submit to the UK Licensing authority in compliance with their Risk Management Strategy. A cost recovery charge is made for these reports. David J. Litt – Public Health England (PHE), now the UK Health Security Agency (UKHSA) Immunisation and Vaccine Preventable Diseases Division provides vaccine manufacturers with post-marketing surveillance reports, which Marketing Authorisation Holders are required to submit to the UK Licensing authority in compliance with their Risk Management Strategy. A cost recovery charge is made for these reports. Zahin Amin-Chowdhury – Public Health England (PHE), now the UK Health Security Agency (UKHSA) Immunisation and Vaccine Preventable Diseases Division provides vaccine manufacturers with post-marketing surveillance reports, which Marketing Authorisation Holders are required to submit to the UK Licensing authority in compliance with their Risk Management Strategy. A cost recovery charge is made for these reports. Marta Bertran – Public Health England (PHE), now the UK Health Security Agency (UKHSA) Immunisation and Vaccine Preventable Diseases Division provides vaccine manufacturers with post-marketing surveillance reports, which Marketing Authorisation Holders are required to submit to the UK Licensing authority in compliance with their Risk Management Strategy. A cost recovery charge is made for these reports. Shamez Ladhani – Public Health England (PHE), now the UK Health Security Agency (UKHSA) Immunisation and Vaccine Preventable Diseases Division provides vaccine manufacturers with post-marketing surveillance reports, which Marketing Authorisation Holders are required to submit to the UK Licensing authority in compliance with their Risk Management Strategy. A cost recovery charge is made for these reports. Catherine Satzke – Lead investigator on a Merck Investigator Studies ProgramProgramme grant funded by MSD on pneumococcal serotype epidemiology. Investigator on a clinical research collaboration on PCV vaccination in Mongolia. Norman K. Fry – Public Health England (PHE), now the UK Health Security Agency (UKHSA) Immunisation and Vaccine Preventable Diseases Division provides vaccine manufacturers with post-marketing surveillance reports, which Marketing Authorisation Holders are required to submit to the UK Licensing authority in compliance with their Risk Management Strategy. A cost recovery charge is made for these reports. Dr NK Fry and his team conduct contract research for pharmaceutical industries on behalf of UKHSA (formerly PHE). No personal remuneration is received. Publisher Copyright: © 2022, Microbiology Society. All rights reserved.

PY - 2022

Y1 - 2022

N2 - Determination of serotypes of Streptococcus pneumoniae is essential for monitoring current vaccine programmes. Since October 2017, pneumococcal serotypes in England have been derived from whole genome sequencing (WGS) data using our bioinformatic tool PneumoCaT. That tool was designed for serotype determination from pure cultures in a reference laboratory. To help determine multiple serotypes in pneumococcal carriage samples, we developed a new software tool named PneumoK-ITy (Pneumococcal K-mer Integrated Typing) that uses the powerful Mash k-mer screening method for pneumococcal serotyp-ing. Mash k-mer screening is more sequence specific and much faster than the mapping method used in PneumoCaT and can determine 54 (58.1 %) of the 93 serotypes in the SSI Diagnostica phenotypical serotyping scheme to type level with the remain-der called to serogroup or subgroup level (e.g., 11A/D). PneumoKITy can be run on both FastQ and assembly input, requiring up to 11× less memory and running up to 29× faster than the current version of PneumoCaT (1.2.1) on FastQ files. PneumoK-ITy can be used as a rapid, flexible serotype screening method which adds sensitive detection of mixed serotypes, e.g., for nasopharyngeal carriage studies where the presence of multiple serotypes is common. PneumoKITy’s ability to function from assembly file, for pure culture serotype detection, increases its speed. This speed potentially enables the software to be run using low infrastructure overhead via web-based platforms. PneumoKITy could be used as a fast initial screening method with other tools used for those serotypes that could not be fully determined to type level if necessary. PneumoKITy was found to be highly accurate and sensitive when run on a panel of FastQ files derived from mixed cultures with all serotypes in 47/51 (92.2 %) of samples being accurately detected. PneumoKITy was also able to accurately estimate the relative abundance of serotypes in the same sample. Estimates being within a mean relative abundance of 1.5 % of the expected abundance in mixtures with known concentrations. PneumoKITy was able to detect minor serotypes with expected abundance of 1 % in the known mixture serotypes. PneumoKITy is a rapid, flexible tool with wide-ranging applications outside of the pure-culture, reference laboratory serotyping remit of PneumoCaT.

AB - Determination of serotypes of Streptococcus pneumoniae is essential for monitoring current vaccine programmes. Since October 2017, pneumococcal serotypes in England have been derived from whole genome sequencing (WGS) data using our bioinformatic tool PneumoCaT. That tool was designed for serotype determination from pure cultures in a reference laboratory. To help determine multiple serotypes in pneumococcal carriage samples, we developed a new software tool named PneumoK-ITy (Pneumococcal K-mer Integrated Typing) that uses the powerful Mash k-mer screening method for pneumococcal serotyp-ing. Mash k-mer screening is more sequence specific and much faster than the mapping method used in PneumoCaT and can determine 54 (58.1 %) of the 93 serotypes in the SSI Diagnostica phenotypical serotyping scheme to type level with the remain-der called to serogroup or subgroup level (e.g., 11A/D). PneumoKITy can be run on both FastQ and assembly input, requiring up to 11× less memory and running up to 29× faster than the current version of PneumoCaT (1.2.1) on FastQ files. PneumoK-ITy can be used as a rapid, flexible serotype screening method which adds sensitive detection of mixed serotypes, e.g., for nasopharyngeal carriage studies where the presence of multiple serotypes is common. PneumoKITy’s ability to function from assembly file, for pure culture serotype detection, increases its speed. This speed potentially enables the software to be run using low infrastructure overhead via web-based platforms. PneumoKITy could be used as a fast initial screening method with other tools used for those serotypes that could not be fully determined to type level if necessary. PneumoKITy was found to be highly accurate and sensitive when run on a panel of FastQ files derived from mixed cultures with all serotypes in 47/51 (92.2 %) of samples being accurately detected. PneumoKITy was also able to accurately estimate the relative abundance of serotypes in the same sample. Estimates being within a mean relative abundance of 1.5 % of the expected abundance in mixtures with known concentrations. PneumoKITy was able to detect minor serotypes with expected abundance of 1 % in the known mixture serotypes. PneumoKITy is a rapid, flexible tool with wide-ranging applications outside of the pure-culture, reference laboratory serotyping remit of PneumoCaT.

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KW - software

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PneumoKITy: A fast, flexible, specific, and sensitive tool for Streptococcus pneumoniae serotype screening and mixed serotype detection from genome sequence data

Abstract

Bibliographical note

Keywords

UN SDGs

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