Microscopy-based phenotypic profiling of infection by Staphylococcus aureus clinical isolates reveals intracellular lifestyle as a prevalent feature

Ines Rodrigues Lopes; Laura Maria Alcantara; Ricardo Jorge Silva; Jerome Josse; Elena Pedrero Vega; Ana Marina Cabrerizo; Melanie Bonhomme; Daniel Lopez; Frederic Laurent; Francois Vandenesch; Miguel Mano; Ana Eulalio

doi:10.1038/s41467-022-34790-9

Microscopy-based phenotypic profiling of infection by Staphylococcus aureus clinical isolates reveals intracellular lifestyle as a prevalent feature

Ines Rodrigues Lopes
, Laura Maria Alcantara
, Ricardo Jorge Silva
, Jerome Josse
, Elena Pedrero Vega
, Ana Marina Cabrerizo
, Melanie Bonhomme
, Daniel Lopez
, Frederic Laurent
, Francois Vandenesch
, Miguel Mano
, Ana Eulalio^*

^*Corresponding author for this work

SCMMS Denmark Hill

University of Coimbra
Université Lyon 1
CSIC Spanish National Research Council
CHU de Lyon
Functional Genomics and RNA-based Therapeutics Laboratory
Department of Life Sciences
University of Coimbra Hospital
School of Cardiovascular Medicine & Sciences
King's British Heart Foundation Centre, King's College London
University of Aveiro
Imperial College London

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

32 Citations (Scopus)

Abstract

Staphylococcus aureus is increasingly recognized as a facultative intracellular pathogen, although the significance and pervasiveness of its intracellular lifestyle remain controversial. Here, we applied fluorescence microscopy-based infection assays and automated image analysis to profile the interaction of 191 S. aureus isolates from patients with bone/joint infections, bacteremia, and infective endocarditis, with four host cell types, at five times post-infection. This multiparametric analysis revealed that almost all isolates are internalized and that a large fraction replicate and persist within host cells, presenting distinct infection profiles in non-professional vs. professional phagocytes. Phenotypic clustering highlighted interesting sub-groups, including one comprising isolates exhibiting high intracellular replication and inducing delayed host death in vitro and in vivo. These isolates are deficient for the cysteine protease staphopain A. This study establishes S. aureus intracellular lifestyle as a prevalent feature of infection, with potential implications for the effective treatment of staphylococcal infections.

Original language	English
Article number	7174
Journal	Nature Communications
Volume	13
Issue number	1
Early online date	22 Nov 2022
DOIs	https://doi.org/10.1038/s41467-022-34790-9
Publication status	Published - Dec 2022

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Rodrigues Lopes, I., Alcantara, L. M., Silva, R. J., Josse, J., Vega, E. P., Cabrerizo, A. M., Bonhomme, M., Lopez, D., Laurent, F., Vandenesch, F., Mano, M., & Eulalio, A. (2022). Microscopy-based phenotypic profiling of infection by Staphylococcus aureus clinical isolates reveals intracellular lifestyle as a prevalent feature. Nature Communications, 13(1), Article 7174. https://doi.org/10.1038/s41467-022-34790-9

@article{a4dbde3913db46f0abdee85555d7aa97,

title = "Microscopy-based phenotypic profiling of infection by Staphylococcus aureus clinical isolates reveals intracellular lifestyle as a prevalent feature",

abstract = "Staphylococcus aureus is increasingly recognized as a facultative intracellular pathogen, although the significance and pervasiveness of its intracellular lifestyle remain controversial. Here, we applied fluorescence microscopy-based infection assays and automated image analysis to profile the interaction of 191 S. aureus isolates from patients with bone/joint infections, bacteremia, and infective endocarditis, with four host cell types, at five times post-infection. This multiparametric analysis revealed that almost all isolates are internalized and that a large fraction replicate and persist within host cells, presenting distinct infection profiles in non-professional vs. professional phagocytes. Phenotypic clustering highlighted interesting sub-groups, including one comprising isolates exhibiting high intracellular replication and inducing delayed host death in vitro and in vivo. These isolates are deficient for the cysteine protease staphopain A. This study establishes S. aureus intracellular lifestyle as a prevalent feature of infection, with potential implications for the effective treatment of staphylococcal infections.",

author = "\{Rodrigues Lopes\}, Ines and Alcantara, \{Laura Maria\} and Silva, \{Ricardo Jorge\} and Jerome Josse and Vega, \{Elena Pedrero\} and Cabrerizo, \{Ana Marina\} and Melanie Bonhomme and Daniel Lopez and Frederic Laurent and Francois Vandenesch and Miguel Mano and Ana Eulalio",

note = "Funding Information: I.R.L. and R.J.S. are recipients of PhD fellowships (PD/BD/146464/2019 and PD/BD/129294/2017) of the Doctoral Program in Experimental Biology and Biomedicine of the Center for Neuroscience and Cell Biology, University of Coimbra. We thank Martin J. Fraunholz (University of W{\"u}rzburg) for providing the pLVTHM-H2B-BFP-IRES-mRFP-CWT plasmid, and Ian Monk (University of Melbourne, Australia) for the E. coli IM08B and IM01B strains. This work was supported by grants from the European Union{\textquoteright}s Horizon 2020 research and innovation program (under the Marie Sk{\l}odowska-Curie grant agreement No 893942 to L.M.A), ERA-NET Infect-ERA StaphIN (031L0094, BMBF, Germany, to A.E.; Infect-ERA/0001/2015, FCT, Portugal, to M.M.; PCIN-2015-151, MINECO, Spain, to D.L.; and ANR 15-IFEC-0002-04, France, to F.L. and F.V), and the ERDF—European Regional Development Fund through COMPETE 2020 and Portuguese Foundation for Science and Technology (POCI-01-0145-FEDER-007440, UIDB/04539/2020, POCI-01-0145-FEDER-029999 to M.M. and A.E.). Funding Information: I.R.L. and R.J.S. are recipients of PhD fellowships (PD/BD/146464/2019 and PD/BD/129294/2017) of the Doctoral Program in Experimental Biology and Biomedicine of the Center for Neuroscience and Cell Biology, University of Coimbra. We thank Martin J. Fraunholz (University of W{\"u}rzburg) for providing the pLVTHM-H2B-BFP-IRES-mRFP-CWT plasmid, and Ian Monk (University of Melbourne, Australia) for the E. coli IM08B and IM01B strains. This work was supported by grants from the European Union{\textquoteright}s Horizon 2020 research and innovation program (under the Marie Sk{\l}odowska-Curie grant agreement No 893942 to L.M.A), ERA-NET Infect-ERA StaphIN (031L0094, BMBF, Germany, to A.E.; Infect-ERA/0001/2015, FCT, Portugal, to M.M.; PCIN-2015-151, MINECO, Spain, to D.L.; and ANR 15-IFEC-0002-04, France, to F.L. and F.V), and the ERDF—European Regional Development Fund through COMPETE 2020 and Portuguese Foundation for Science and Technology (POCI-01-0145-FEDER-007440, UIDB/04539/2020, POCI-01-0145-FEDER-029999 to M.M. and A.E.). Publisher Copyright: {\textcopyright} 2022, The Author(s).",

year = "2022",

month = dec,

doi = "10.1038/s41467-022-34790-9",

language = "English",

volume = "13",

journal = "Nature Communications",

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Rodrigues Lopes, I, Alcantara, LM, Silva, RJ, Josse, J, Vega, EP, Cabrerizo, AM, Bonhomme, M, Lopez, D, Laurent, F, Vandenesch, F, Mano, M & Eulalio, A 2022, 'Microscopy-based phenotypic profiling of infection by Staphylococcus aureus clinical isolates reveals intracellular lifestyle as a prevalent feature', Nature Communications, vol. 13, no. 1, 7174. https://doi.org/10.1038/s41467-022-34790-9

TY - JOUR

T1 - Microscopy-based phenotypic profiling of infection by Staphylococcus aureus clinical isolates reveals intracellular lifestyle as a prevalent feature

AU - Rodrigues Lopes, Ines

AU - Alcantara, Laura Maria

AU - Silva, Ricardo Jorge

AU - Josse, Jerome

AU - Vega, Elena Pedrero

AU - Cabrerizo, Ana Marina

AU - Bonhomme, Melanie

AU - Lopez, Daniel

AU - Laurent, Frederic

AU - Vandenesch, Francois

AU - Mano, Miguel

AU - Eulalio, Ana

N1 - Funding Information: I.R.L. and R.J.S. are recipients of PhD fellowships (PD/BD/146464/2019 and PD/BD/129294/2017) of the Doctoral Program in Experimental Biology and Biomedicine of the Center for Neuroscience and Cell Biology, University of Coimbra. We thank Martin J. Fraunholz (University of Würzburg) for providing the pLVTHM-H2B-BFP-IRES-mRFP-CWT plasmid, and Ian Monk (University of Melbourne, Australia) for the E. coli IM08B and IM01B strains. This work was supported by grants from the European Union’s Horizon 2020 research and innovation program (under the Marie Skłodowska-Curie grant agreement No 893942 to L.M.A), ERA-NET Infect-ERA StaphIN (031L0094, BMBF, Germany, to A.E.; Infect-ERA/0001/2015, FCT, Portugal, to M.M.; PCIN-2015-151, MINECO, Spain, to D.L.; and ANR 15-IFEC-0002-04, France, to F.L. and F.V), and the ERDF—European Regional Development Fund through COMPETE 2020 and Portuguese Foundation for Science and Technology (POCI-01-0145-FEDER-007440, UIDB/04539/2020, POCI-01-0145-FEDER-029999 to M.M. and A.E.). Funding Information: I.R.L. and R.J.S. are recipients of PhD fellowships (PD/BD/146464/2019 and PD/BD/129294/2017) of the Doctoral Program in Experimental Biology and Biomedicine of the Center for Neuroscience and Cell Biology, University of Coimbra. We thank Martin J. Fraunholz (University of Würzburg) for providing the pLVTHM-H2B-BFP-IRES-mRFP-CWT plasmid, and Ian Monk (University of Melbourne, Australia) for the E. coli IM08B and IM01B strains. This work was supported by grants from the European Union’s Horizon 2020 research and innovation program (under the Marie Skłodowska-Curie grant agreement No 893942 to L.M.A), ERA-NET Infect-ERA StaphIN (031L0094, BMBF, Germany, to A.E.; Infect-ERA/0001/2015, FCT, Portugal, to M.M.; PCIN-2015-151, MINECO, Spain, to D.L.; and ANR 15-IFEC-0002-04, France, to F.L. and F.V), and the ERDF—European Regional Development Fund through COMPETE 2020 and Portuguese Foundation for Science and Technology (POCI-01-0145-FEDER-007440, UIDB/04539/2020, POCI-01-0145-FEDER-029999 to M.M. and A.E.). Publisher Copyright: © 2022, The Author(s).

PY - 2022/12

Y1 - 2022/12

N2 - Staphylococcus aureus is increasingly recognized as a facultative intracellular pathogen, although the significance and pervasiveness of its intracellular lifestyle remain controversial. Here, we applied fluorescence microscopy-based infection assays and automated image analysis to profile the interaction of 191 S. aureus isolates from patients with bone/joint infections, bacteremia, and infective endocarditis, with four host cell types, at five times post-infection. This multiparametric analysis revealed that almost all isolates are internalized and that a large fraction replicate and persist within host cells, presenting distinct infection profiles in non-professional vs. professional phagocytes. Phenotypic clustering highlighted interesting sub-groups, including one comprising isolates exhibiting high intracellular replication and inducing delayed host death in vitro and in vivo. These isolates are deficient for the cysteine protease staphopain A. This study establishes S. aureus intracellular lifestyle as a prevalent feature of infection, with potential implications for the effective treatment of staphylococcal infections.

AB - Staphylococcus aureus is increasingly recognized as a facultative intracellular pathogen, although the significance and pervasiveness of its intracellular lifestyle remain controversial. Here, we applied fluorescence microscopy-based infection assays and automated image analysis to profile the interaction of 191 S. aureus isolates from patients with bone/joint infections, bacteremia, and infective endocarditis, with four host cell types, at five times post-infection. This multiparametric analysis revealed that almost all isolates are internalized and that a large fraction replicate and persist within host cells, presenting distinct infection profiles in non-professional vs. professional phagocytes. Phenotypic clustering highlighted interesting sub-groups, including one comprising isolates exhibiting high intracellular replication and inducing delayed host death in vitro and in vivo. These isolates are deficient for the cysteine protease staphopain A. This study establishes S. aureus intracellular lifestyle as a prevalent feature of infection, with potential implications for the effective treatment of staphylococcal infections.

UR - https://www.scopus.com/pages/publications/85142501133

U2 - 10.1038/s41467-022-34790-9

DO - 10.1038/s41467-022-34790-9

M3 - Article

AN - SCOPUS:85142501133

SN - 2041-1723

VL - 13

JO - Nature Communications

JF - Nature Communications

IS - 1

M1 - 7174

ER -

Microscopy-based phenotypic profiling of infection by Staphylococcus aureus clinical isolates reveals intracellular lifestyle as a prevalent feature

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