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Analysis of institutional authors

Nunez-Rodriguez JcAuthorSchikora-Tamarit MàAuthorKsiezopolska EAuthorGabaldon, ToniCorresponding Author

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May 23, 2025
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Simple large-scale quantitative phenotyping and antimicrobial susceptibility testing with Q-PHAST

Publicated to: Nature Protocols. - 2025-05-12 (), DOI: 10.1038/s41596-025-01179-z

Authors:

Nunez-Rodriguez, Juan Carlos; Schikora-Tamarit, Miquel angel; Ksiezopolska, Ewa; Gabaldon, Toni
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Affiliations

Barcelona Inst Sci & Technol, Inst Res Biomed IRB Barcelona, Barcelona, Spain - Author
Barcelona Supercomp Ctr BSC CNS, Barcelona, Spain - Author
Catalan Inst Res & Adv Studies ICREA, Barcelona, Spain - Author
Comparative Genomics. Institute for Research in Biomedicine - Author
Inst Salud Carlos III, CIBER Enfermedades Infecciosas, Madrid, Spain - Author
Institute for Research in Biomedicine - Author
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Abstract

The characterization of antimicrobial susceptibility and other relevant phenotypes in large collections of microbial isolates is a common need across research and clinical microbiology laboratories. Robotization provides unprecedented throughput but involves costs that are prohibitive for the average laboratory. Here, using affordable materials and open-source software, we developed Q-PHAST (Quantitative PHenotyping and Antimicrobial Susceptibility Testing), a unique solution for cost-effective, large-scale phenotyping in a standard microbiology laboratory. Single colonies are grown in a deep 96-well master plate, from which diluted aliquots are used to generate 96 spots on different experimental plates containing solid medium with the substance and concentration of interest. These plates are incubated on inexpensive flatbed scanners that monitor the growth of each spot by obtaining images every 15 min. A simple, python-based software, which can be used via a graphical interface on various operating systems (https://github.com/Gabaldonlab/Q-PHAST), analyzes the images to infer growth, fitness (e.g., doubling rate) and susceptibility (e.g., minimum inhibitory concentration) measures. With
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Quality index

Bibliometric impact. Analysis of the contribution and dissemination channel

The work has been published in the journal Nature Protocols due to its progression and the good impact it has achieved in recent years, according to the agency WoS (JCR), it has become a reference in its field. In the year of publication of the work, 2025, it was in position 2/86, thus managing to position itself as a Q1 (Primer Cuartil), in the category Biochemical Research Methods. Notably, the journal is positioned above the 90th percentile.

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Impact and social visibility

From the perspective of influence or social adoption, and based on metrics associated with mentions and interactions provided by agencies specializing in calculating the so-called "Alternative or Social Metrics," we can highlight as of 2025-12-30:

  • The use, from an academic perspective evidenced by the Altmetric agency indicator referring to aggregations made by the personal bibliographic manager Mendeley, gives us a total of: 3.
  • The use of this contribution in bookmarks, code forks, additions to favorite lists for recurrent reading, as well as general views, indicates that someone is using the publication as a basis for their current work. This may be a notable indicator of future more formal and academic citations. This claim is supported by the result of the "Capture" indicator, which yields a total of: 1 (PlumX).

With a more dissemination-oriented intent and targeting more general audiences, we can observe other more global scores such as:

  • The Total Score from Altmetric: 4.
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Leadership analysis of institutional authors

There is a significant leadership presence as some of the institution’s authors appear as the first or last signer, detailed as follows: First Author (NÚÑEZ RODRÍGUEZ, Juan Carlos) and Last Author (Gabaldon Esteban, Toni).

the author responsible for correspondence tasks has been Gabaldon Esteban, Toni.

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Awards linked to the item

The T.G. group acknowledges support from the Spanish Ministry of Science and Innovation for grants PID2021-126067NB-I00, CPP2021-008552, PCI2022-135066-2 and PDC2022-133266-I00, cofounded by ERDF 'A way of making Europe'; from the Catalan Research Agency (AGAUR) SGR01551; from the European Union's Horizon 2020 research and innovation programme (ERC-2016-724173); from the Gordon and Betty Moore Foundation (grant GBMF9742); from the 'La Caixa' Foundation (grant LCF/PR/HR21/00737); and from the Instituto de Salud Carlos III (IMPACT grant IMP/00019 and CIBERINFEC CB21/13/00061-ISCIII-SGEFI/ERDF). J.C.N.-R. received a predoctoral fellowship from the Spanish Ministry of Science and Innovation (grant number PRE2019-088193). M.A.S.-T. received a predoctoral fellowship from the 'La Caixa' Foundation (grant LCF/BQ/DR19/11740023). Some of the figures were created with BioRender.com The authors thank all of the members of the T.G. group for key support during this work. The authors particularly thank V. d. Olmo, I. Ahaik, D. Fuentes, E. Saus and M. Bernabeu, who provided useful feedback, which was key for the project development.
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