Time-Resolved Transposon Insertion Sequencing Reveals Genome-Wide Fitness Dynamics during Infection

ABSTRACT Transposon insertion sequencing (TIS) is a powerful high-throughput genetic technique that is transforming functional genomics in prokaryotes, because it enables genome-wide mapping of the determinants of fitness. However, current approaches for analyzing TIS data assume that selective pres...

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Autores principales:	Guanhua Yang, Gabriel Billings, Troy P. Hubbard, Joseph S. Park, Ka Yin Leung, Qin Liu, Brigid M. Davis, Yuanxing Zhang, Qiyao Wang, Matthew K. Waldor
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2017
Materias:	Edwardsiella piscicida live attenuated vaccine pattern analysis of conditional essentiality (PACE) transposon insertion sequencing fitness dynamics and profiles Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/6c4aa7aa57ee46f5895f9fbddd29f3ce
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spelling	oai:doaj.org-article:6c4aa7aa57ee46f5895f9fbddd29f3ce2021-11-15T15:51:50ZTime-Resolved Transposon Insertion Sequencing Reveals Genome-Wide Fitness Dynamics during Infection10.1128/mBio.01581-172150-7511https://doaj.org/article/6c4aa7aa57ee46f5895f9fbddd29f3ce2017-11-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mBio.01581-17https://doaj.org/toc/2150-7511ABSTRACT Transposon insertion sequencing (TIS) is a powerful high-throughput genetic technique that is transforming functional genomics in prokaryotes, because it enables genome-wide mapping of the determinants of fitness. However, current approaches for analyzing TIS data assume that selective pressures are constant over time and thus do not yield information regarding changes in the genetic requirements for growth in dynamic environments (e.g., during infection). Here, we describe structured analysis of TIS data collected as a time series, termed pattern analysis of conditional essentiality (PACE). From a temporal series of TIS data, PACE derives a quantitative assessment of each mutant’s fitness over the course of an experiment and identifies mutants with related fitness profiles. In so doing, PACE circumvents major limitations of existing methodologies, specifically the need for artificial effect size thresholds and enumeration of bacterial population expansion. We used PACE to analyze TIS samples of Edwardsiella piscicida (a fish pathogen) collected over a 2-week infection period from a natural host (the flatfish turbot). PACE uncovered more genes that affect E. piscicida’s fitness in vivo than were detected using a cutoff at a terminal sampling point, and it identified subpopulations of mutants with distinct fitness profiles, one of which informed the design of new live vaccine candidates. Overall, PACE enables efficient mining of time series TIS data and enhances the power and sensitivity of TIS-based analyses. IMPORTANCE Transposon insertion sequencing (TIS) enables genome-wide mapping of the genetic determinants of fitness, typically based on observations at a single sampling point. Here, we move beyond analysis of endpoint TIS data to create a framework for analysis of time series TIS data, termed pattern analysis of conditional essentiality (PACE). We applied PACE to identify genes that contribute to colonization of a natural host by the fish pathogen Edwardsiella piscicida. PACE uncovered more genes that affect E. piscicida’s fitness in vivo than were detected using a terminal sampling point, and its clustering of mutants with related fitness profiles informed design of new live vaccine candidates. PACE yields insights into patterns of fitness dynamics and circumvents major limitations of existing methodologies. Finally, the PACE method should be applicable to additional “omic” time series data, including screens based on clustered regularly interspaced short palindromic repeats with Cas9 (CRISPR/Cas9).Guanhua YangGabriel BillingsTroy P. HubbardJoseph S. ParkKa Yin LeungQin LiuBrigid M. DavisYuanxing ZhangQiyao WangMatthew K. WaldorAmerican Society for MicrobiologyarticleEdwardsiella piscicidalive attenuated vaccinepattern analysis of conditional essentiality (PACE)transposon insertion sequencingfitness dynamics and profilesMicrobiologyQR1-502ENmBio, Vol 8, Iss 5 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Edwardsiella piscicida live attenuated vaccine pattern analysis of conditional essentiality (PACE) transposon insertion sequencing fitness dynamics and profiles Microbiology QR1-502
spellingShingle	Edwardsiella piscicida live attenuated vaccine pattern analysis of conditional essentiality (PACE) transposon insertion sequencing fitness dynamics and profiles Microbiology QR1-502 Guanhua Yang Gabriel Billings Troy P. Hubbard Joseph S. Park Ka Yin Leung Qin Liu Brigid M. Davis Yuanxing Zhang Qiyao Wang Matthew K. Waldor Time-Resolved Transposon Insertion Sequencing Reveals Genome-Wide Fitness Dynamics during Infection
description	ABSTRACT Transposon insertion sequencing (TIS) is a powerful high-throughput genetic technique that is transforming functional genomics in prokaryotes, because it enables genome-wide mapping of the determinants of fitness. However, current approaches for analyzing TIS data assume that selective pressures are constant over time and thus do not yield information regarding changes in the genetic requirements for growth in dynamic environments (e.g., during infection). Here, we describe structured analysis of TIS data collected as a time series, termed pattern analysis of conditional essentiality (PACE). From a temporal series of TIS data, PACE derives a quantitative assessment of each mutant’s fitness over the course of an experiment and identifies mutants with related fitness profiles. In so doing, PACE circumvents major limitations of existing methodologies, specifically the need for artificial effect size thresholds and enumeration of bacterial population expansion. We used PACE to analyze TIS samples of Edwardsiella piscicida (a fish pathogen) collected over a 2-week infection period from a natural host (the flatfish turbot). PACE uncovered more genes that affect E. piscicida’s fitness in vivo than were detected using a cutoff at a terminal sampling point, and it identified subpopulations of mutants with distinct fitness profiles, one of which informed the design of new live vaccine candidates. Overall, PACE enables efficient mining of time series TIS data and enhances the power and sensitivity of TIS-based analyses. IMPORTANCE Transposon insertion sequencing (TIS) enables genome-wide mapping of the genetic determinants of fitness, typically based on observations at a single sampling point. Here, we move beyond analysis of endpoint TIS data to create a framework for analysis of time series TIS data, termed pattern analysis of conditional essentiality (PACE). We applied PACE to identify genes that contribute to colonization of a natural host by the fish pathogen Edwardsiella piscicida. PACE uncovered more genes that affect E. piscicida’s fitness in vivo than were detected using a terminal sampling point, and its clustering of mutants with related fitness profiles informed design of new live vaccine candidates. PACE yields insights into patterns of fitness dynamics and circumvents major limitations of existing methodologies. Finally, the PACE method should be applicable to additional “omic” time series data, including screens based on clustered regularly interspaced short palindromic repeats with Cas9 (CRISPR/Cas9).
format	article
author	Guanhua Yang Gabriel Billings Troy P. Hubbard Joseph S. Park Ka Yin Leung Qin Liu Brigid M. Davis Yuanxing Zhang Qiyao Wang Matthew K. Waldor
author_facet	Guanhua Yang Gabriel Billings Troy P. Hubbard Joseph S. Park Ka Yin Leung Qin Liu Brigid M. Davis Yuanxing Zhang Qiyao Wang Matthew K. Waldor
author_sort	Guanhua Yang
title	Time-Resolved Transposon Insertion Sequencing Reveals Genome-Wide Fitness Dynamics during Infection
title_short	Time-Resolved Transposon Insertion Sequencing Reveals Genome-Wide Fitness Dynamics during Infection
title_full	Time-Resolved Transposon Insertion Sequencing Reveals Genome-Wide Fitness Dynamics during Infection
title_fullStr	Time-Resolved Transposon Insertion Sequencing Reveals Genome-Wide Fitness Dynamics during Infection
title_full_unstemmed	Time-Resolved Transposon Insertion Sequencing Reveals Genome-Wide Fitness Dynamics during Infection
title_sort	time-resolved transposon insertion sequencing reveals genome-wide fitness dynamics during infection
publisher	American Society for Microbiology
publishDate	2017
url	https://doaj.org/article/6c4aa7aa57ee46f5895f9fbddd29f3ce
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Time-Resolved Transposon Insertion Sequencing Reveals Genome-Wide Fitness Dynamics during Infection

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