The Clinical and Experimental Microbiology Unit (UMCIE), led by Dr Pere-Joan Cardona, Head of the Microbiology Service at Germans Trias i Pujol University Hsopital (HUGTiP), constitutes a consolidated multidisciplinary research group accredited by the Catalan Government. The Group has been involved in the Spanish research networks REIPI (Red Española de Centros de Investigación en Patología Infecciosa), RESITRA (Redes de Grupos de Infección y Trasplante), and currently several group members belong to CIBERES (Centro de Investigación Biomédica en Red en Enfermedades Respiratorias) while some others belong to CIBERESP (Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública).

The research group focuses its activity in the development, standardisation and clinical evaluation of microbiological, immunological and molecular techniques susceptible to be used in the diagnosis of infectious diseases, together with the development of in vivo experimental models including the Drosophila model, to understand the host-pathogen interface, especially in coinfections; the study of the molecular mechanisms underlying antimicrobial resistance, the assessment of the antimicrobial activity of new antiseptic and disinfectants, and the fight against nosocomial infection through classic and genomic epidemiology tools. Genomic epidemiology through whole genome sequencing has also been applied to pathogens of public health interest, such as Mycobacterium tuberculosis (as reference centre in Catalonia) or SARS-CoV-2, for surveillance purposes and especially for the characterisation of outbreaks. NSG has also provided the opportunity for refining diagnosis, through amplifying and sequencing ribosomal 16S in difficult samples (such as cardiac valves or LCR); or to analyse gut microbiota to evaluate its impact in several pathologies. Finally, the group is also very active in refining new tools for screening sexual transmitted diseases both in general and high risk populations.

The intense activity in R+D during the last 25 years has encouraged several scientists from the hospital service to develop their own career as independent groups within the IGTP, these are the Experimental Tuberculosis Unit (Cristina Vilaplana); Pathogen Diagnostics and Genomic Epidemiology (Elisa Martró) and Innovation in Respiratory Infections and Tuberculosis Diagnosis (José Domínguez & Cristina Prat), with whom the group collaborates very closely.

The group aims to be the reference for the "pathogen view" on the Can Ruti Campus. This is possible due to its privileged view of daily service in the hospital collaborating with the medical staff in the diagnosis, prophylaxis and treatment of infectious diseases. The group has a strong tradition of cooperating and networking and offers to collaborate with all IGTP’s research groups and the School of Medicine of UAB, to link the magic triangle of healthcare, research and education. In addition, the group has the ambition of being a reference for innovation and tech-transfer activities on the campus.

Keywords: Tuberculosis, virology, emerging infections, STD, host-pathogen interface, molecular epidemiology, NGS, gut microbiota.

Microbiology Service Germans Trias i Pujol University Hospital June 2021

Group leader

  • Pere-Joan Cardona, MD, PhD
    Pere-Joan Cardona, MD, PhD

    Pere-Joan Cardona, MD, PhD

    Pere-Joan Cardona serves as the Chief of the Microbiology Department at Germans Trias i Pujol University Hospital, which is part of Institut Català de la Salut (ICS). He also holds the position of Professor at Universitat Autònoma de Barcelona. With over 25 years of experience, he is a clinical microbiologist dedicated to unravelling the mechanisms underlying latent tuberculosis infection and the transition to active tuberculosis (TB).

    To advance his research efforts, Pere-Joan Cardona founded the Experimental Tuberculosis Unit at Germans Trias i Pujol Research Institute (IGTP). His work has been instrumental in developing innovative in vivo and in silico experimental models, making substantial contributions to the field. Notably, his research resulted in the creation of the RUTI therapeutic vaccine and the exploration of host-directed therapies for tackling TB. Additionally, he has delved into the immunomodulatory properties of environmental mycobacteria, with the goal of harmonizing immune responses to combat various diseases.

    Pere-Joan Cardona possesses extensive expertise in leading clinical trials aimed at developing novel diagnostic, prophylactic, and therapeutic tools for tuberculosis. His active collaboration with international consortiums dedicated to TB research underscores his dedication to advancing our understanding of this global health issue.

    Once appointed as Chief of the Department, Pere-Joan Cardona has added some other interests to his goals. On the one hand, the use of NSG for a molecular epidemiology program aimed to curtail the dissemination of M. tuberculosis clusters in Catalonia, which is funded and part of the Catalan Public Health Agency; the amplification of 16S for complex clinical samples and the characterisation of the gut microbiota in different pathologies. He is also very interested in refining better tools for STD screening in general and high-risk populations. Finally, he is extending the experimental infection model in Drosophila to other pathogens, such us Enterococcus, Pseudomonas aeruginosa, Staphylococcus aureus and Candida albicans, to better understand the host-pathogen interface.

    Contact: pcardonai.germanstrias(ELIMINAR)@gencat.cat
    ORCID: 0000-0001-5623-7873

Research lines

The group has formulated five strategic objectives for the coming years.

Development of 6 strategic lines

Response to challenges related to virology

  • SARS-CoV-2: Since early 2021, the group has actively participated in surveillance through genomic epidemiology, which enables the rapid detection of virus variants associated with increased transmissibility or immune evasion (linked to outbreaks in the context of high vaccination coverage), increased virulence, and the progressive rise of treatment resistance in the short to medium term.
  • Viral hepatitis (B and C): New indicators need to be established to monitor the prevalence and incidence of HCV in people who inject drugs and other vulnerable populations using molecular methods from alternative samples such as dried blood spots. This will enhance accessibility to diagnosis, meeting the WHO's elimination goals for 2030, and designing more effective prevention and control measures. Additionally, the group is evaluating integrated screening strategies for other fluid-transmitted infections in the emergency department population.

Response to challenges related to mycobacteriology

  • Genomic Epidemiology of Mycobacterium tuberculosis Complex (MTBC): The group has initiated a sequencing study of all tuberculosis-causing strains in Catalonia, improving surveillance and enabling the evaluation of genomic profiles linked to chemotherapy resistance and virulence.
  • Study of M. tuberculosis virulence: Through co-evolution studies in D. melanogaster over 10 generations, less virulent M. marinum strains have been generated. Sequencing and transcriptomic analyses of these strains will allow for comparisons with M. tuberculosis.
  • Control of environmental mycobacteria outbreaks: These bacteria pose a growing challenge, and outbreaks need to be characterised; for instance, M. chimerae associated with extracorporeal circulation devices generating aerosols in Coronary Units, and the increasing cases of M. intracellulare and M. abscessus.

Response to challenges related to sexually transmitted infections

  • Molecular epidemiology of syphilis: From 2010 to 2020, the rate of infectious syphilis per 100,000 inhabitants increased by an average of 20% annually in Catalonia. Typing these strains will improve understanding of their spread, virulence profiles, and macrolide resistance.
  • Study of quinolone resistance mechanisms in Mycoplasma genitalium: This bacterium has a prevalence of 1-2% in the general population and 30% in high-risk groups. Resistance to the recommended treatment (azithromycin) is increasing, and the alternative, quinolones, requires genomic characterisation using the material accumulated by the group since 2016.

Response to challenges related to invasive infections

  • Determination of pAmpC plasmid in sepsis: These infections require rapid diagnostic systems and resistance mechanism characterisation. The group is currently validating the T2 BioSystems, which lacks the ability to identify the pAmpC plasmid linked to extended-spectrum beta-lactamase (ESBL) resistance. Only nanopore technology can faithfully characterise the entire plasmid.
  • Diagnosis of meningitis: Diagnostic approaches for these infections must be rapid and capable of detecting a wide range of bacteria, fungi, and viruses. Nanopore sequencing will enable this approach through metagenomic and virome studies.

Response to challenges related to coinfection

  • Interaction between Pseudomonas aeruginosa and Staphylococcus aureus: The synergy between these bacteria is responsible for severe infections such as diabetic foot and pneumonia in intubated patients. Genomic characterisation and the use of the experimental infection model in D. melanogaster will help elucidate the nature of this synergy.
  • Impact of fecal microbiota on the selection of multiresistance: Metagenomic studies will allow evaluation of the impact of intestinal microbiota on the selection of multidrug-resistant strains and can be experimentally studied using intestinal colonisation models in axenic D. melanogaster.

Response to challenges related to antibiotic multiresistance

  • Study of the dissemination of multidrug-resistant bacteria: This includes studying Klebsiella pneumoniae, Enterobacter spp., Escherichia coli, and other bacteria with ESBL and/or carbapenemases, P. aeruginosa, and methicillin-resistant S. aureus (MRSA). The group is validating detection procedures and prospective surveillance in hospitals, seeking phenotypic links (through infrared profiles -IRBiotyper-) or genetic links (NGS) to establish epidemiological connections (outbreaks), while also detecting virulence profiles to characterise highly dangerous strains, with the help of the D. melanogaster model.

Development of NGS techniques and modelling

The development of the strategic lines described in Objective 1 shares the common use of two methodological blocks, which will enable transversal knowledge across all lines:

  • NGS: To perform metagenomics and establish diagnostic tools for samples that are difficult to characterise, either due to the wide range of pathogens involved or the low yield of cultures; and to conduct studies on coinfections and microbiota. Sequencing will allow for the characterisation of resistance and virulence mechanisms and establish homologies between different strains to identify epidemiological links. Metagenomics will also facilitate the study of coinfections and the role of microbiota in the development of various infections.
  • In vivo modelling: This includes the use of infection, coinfection, and co-evolution models in Drosophila melanogaster to study virulence processes and antibiotic resistance selection in vivo. This model can be scaled to a mouse infection model for specific cases. All generated data will be integrated into in silico simulation models to better exploit the data and test hypotheses for falsifiability.

Technology transfer line

The development of the previous two objectives will allow for the generation of a multi-level transfer process, culminating in a symposium where all results from this period will be presented, marking a milestone for all lines and stimulating cross-disciplinary work.

  • Development of new diagnostic and prevention algorithms: Specifically, in the Virology line, this will optimise the detection process of new SARS-CoV-2 variants and improve infection management algorithms. For hepatitis and STIs, simpler sample collection techniques, such as dried blood spots, will be used to reach hard-to-access population groups. Regarding tuberculosis management, the TB-SEQ consortium is designed for transfer to the Catalan Public Health Agency to incorporate it into new active outbreak research strategies. The study of coinfections will improve the management of complex infections in immunocompromised patients. Rapid identification of outbreaks and multidrug resistance will substantially enhance patient treatment and nosocomial infection control.
  • Validation of new techniques in collaboration with industry: The group has established a consistent partnership with the industry, adding value to existing cutting-edge technologies and enabling collaboration agreements. Examples include the incorporation of the IR-Biotyper for rapid management of nosocomial multidrug-resistant outbreaks, Nanopore technology for complex diagnostics, and collaborations with companies such as Beckman, Biomerieux, Abbott, Gilead, Abbvie, and MSD.
  • Generation of intellectual property: The group has extensive experience in generating intellectual property, with 9 invention patents and 3 spin-offs generated by Dr. Cardona. The group is fully integrated into the Catalan biotech ecosystem, aiming to identify opportunities that can generate market opportunities.


In the next three years, the plan is to continue training undergraduate, master's, and doctoral students (10 theses currently registered). Additionally, the group is training two specialists annually through MIR, FIR, and BIR programs, aiming to integrate clinical practice with research and innovation. The group is ideal for identifying problems arising in routine clinical practice that generate Strategic Lines and transferring them to members more focused on basic research, responsible for the methodological blocks. The idea is to promote this collaboration through joint sessions, create mixed working groups to solve challenges, and generate transversal knowledge.


  • Communication at conferences: All group members will be encouraged to periodically present results at key conferences of state and international scientific societies: SEPAR, SEIMC, SCM, FUITB, ECCMID, EASL, and in leading scientific journals.
  • Communication to the public: Especially to encourage scientific spirit in schools and institutes; directed at vulnerable populations and the general public. Both Dr Martró and Dr Cardona are very active in digital forums, being reference specialists and regularly participating in high-impact programs on TV3, TVE, Catalunya Radio, RAC-1, and newspapers like Ara or La Vanguardia.
  • Launch a group blog: The group will disseminate R&I activities and include scientific outreach articles aimed at the general public.

Active projects

Epidemiological modelling of SARS-CoV2 in a post-pandemic surveillance context: an open platform for mid-term scenarios and short-term predictions

PI: Clara Prats Soler
Funding agency: Fundación BBVA
​​​​​​Duration: 01/07/2022 – 30/06/2024

Viabilidad e impacto del cribado online de VIH / ITS dirigido a hombres que tienen sexo con hombres y mujeres transgénero en España usuarios de profilaxis pre-exposición (TÉSTATE-PrEP)

PI: Cristina Agustí Benito
​​​​​​Funding agency: Instituto de Salud Carlos III (ISCIII)
Agency code: PI21/01589
Duration: 2022 - 2024

Una perspectiva global de las enfermedades neumocócicas y la resistencia en tiempos de pandemia por COVID-19 y vacunación universal en pediatría

PIs: Ardanuy Tisaire, Maria Carmen
Funding agency: Instituto de Salud Carlos III (ISCIII)
Agency code: PI21/01000
Duration: 2021 - 2023

Vigilància activa de la Listeriosi a Catalunya a través de l'Epidemiologia molecular

PI: Pere-Joan Cardona
Funding agency: Agència de Salut Pública de Catalunya
Duration: 2021- (renewable annually)

Consolidation of WGS and RT-PCR activities for SARS-CoV-2 in Spain towards sustainable use and integration of enhanced infrastructure and capacities in the RELECOV network.

Funding agency: European Health and Digital Executive Agency (HADEA). EU4H Project Grants
Agency code: EU4H-2022-DGA-MS-IBA-01-02
Duration: 2023 – 2025

SMA-TB:  A novel Stratified Medicine Algorithm to predict treatment responses to host-directed therapy in TB Patients

PI: Cristina Vilaplana
Funding agency: European Community H2020 Programme
Agency code: H2020-SC1-BHC-2018-2020
Duration: 2020 - 2024

Grup de Microbiologia Clínica i Patologia Infecciosa Experimental. Ajuts de suport als grups de recerca consolidats de Catalunya

PI: PJ Cardona
Funding agency: Agència de Gestió d'Ajuts Universitaris i de Recerca (AGAUR). Generalitat de Catalunya
Agency code: 2021 SGR 00931; SGR 2017 477; 2014 SGR 1099; 1999 SGR 0236; 2001 SGR 00461; 2009 SGR 1485; 2005
Duration: 1999 - 2024

TB-SEQ. Vigilància activa de la tuberculosi a Catalunya a través de l'Epidemiologia molecular

PI: Pere-Joan Cardona
Funding agency: Agència de Salut Pública de Catalunya
Duration: 2021- (renewable annually)

Novel immunotherapies for tuberculosis and other mycobacterial diseases (ITHEMYC)

PI: Pere-Joan Cardona
Funding agency: European Health and Digital Executive Agency (HADEA)
Agency code: 101080462
Duration: 2023 – 2026

Past projects

Screening of bloodborne viruses in the emergency department of Hospital Germans Trias i Pujol

PIs: Morillas RMª., Martró E., Carreres Molas A. Negredo E.
Funding agency: Gilead Sciences, S.L.U.
Agency code: FOCUS Program
Duration: 27/06/2022 - 26/06/2023

Population-based genomic epidemiology study for tailored strategies for surveillance and control of tuberculosis (TB-SEQ)

PIs: Elisa Martró, Iñaki Comas
Funding agency: CIBER Enfermedades Respiratorias (CIBERES)
Duration: 24/02/2022 - 31/12/2023

Proyecto de búsqueda activa de pacientes VHC en el Hospital Universitari Germans Trias i Pujol a partir de resultados de Microbiología

PIs: Morillas RMª., Martró E.
Funding agency: Gilead Sciences, S.L.U.
Agency code: FindHCV
Duration: 11/01/2022 - 10/07/2022

Development of Robust and Innovative Vaccine Effectiveness

PIs: Guillermo Mena, Irma Casas
Funding agency: Innovative Medicines Initiative (Call for Tenders 2021/2022)
Agency code: IMI-DRIVE_3
Duration: 15/09/2021 - 30/06/2023

Brand-specific COVID-19 vaccine effectiveness against severe COVID-19 disease in Europe

PI: Guillermo Mena
Funding agency: P-95 CVBA Development Aid
Agency code: COVIDRIVE
Duration: 24/05/2021 - 24/05/2023

Vigilancia semiautomatizada de las infecciones quirúrgicas:  el avance hacia una estrategia mejorada para la prevención y control de las infecciones relacionadas con la atención sanitaria

PI: Juan José Gonzalez Lopez
Funding agency: Instituto de Salud Carlos III (ISCIII)
Agency code: PI21/00862
Duration: 2021 - 2023

Caracterización de Neisseria meningitidis tras la introducción de la vacuna frente al serogrupo B e identificación de factores predisponentes para la enfermedad meningocócica invasiva

PI: Juanjo González López
Funding agency: Instituto de Salud Carlos III (ISCIII)
Agency code: PI21/00132

Estudio de las bases biológicas de la susceptibilidad a la tuberculosis según el sexo. Importancia del eje hipotalámico-pituitarioadrenal

PI: PJ Cardona
Funding agency: Instituto de Salud Carlos III (ISCIII)
Agency code: PI20/01431
Duration: 2021 - 2023

Semi-automated surveillance of surgical site infections:  a step towards enhanced methos in Infection prevention and control

PI: Castellà L.
Funding agency: Instituto de Salud Carlos III (ISCIII)
Agency code: PI20/01563
Duration: 2021 - 2023

Epidemiologia genòmica de SARS-CoV-2 a Catalunya:  vigilància virològica i control de brots

PI: Elisa Matró, Marc Noguera
Funding agency: Fundació Marató TV3
Agency code: 342/C/2021
Duration: 2021 - 2023

Cost-effectiveness of a community intervention versus a healthcare-based strategy for promoting the prevention, diagnosis and treatment of hepatitis B and C in immigrants in Catalonia

PI: Martró E.
Funding agency: Instituto de Salud Carlos III. Ministerio de Sanidad y Consumo
Agency code: PI19/0568
Duration: 01/01/2020 - 31/12/2023

Estratègia comunitària de cribratge de les Hepatitis B i C, i del VIH i accés precoç al tractament, en població migrant provinent de països d'alta prevalença

PI: Clom J.
Funding agency: Gilead Sciences, S.L.U.
Agency code: MiCATC
Duration: 01/05/2020 - 01/06/2022

Prevenció de la bacterièmia de catèter a les unitats d'hospitalització convencional

PI: O. Guarch
Funding agency: Instituto de Salud Carlos III (ISCIII)
Agency code: PI20/01563
Duration: 2020 - 2022

Program for the progressive substitution of laboratory animals in the Center for Comparative Medicine (IGTP) (CMCiB-3R)

PI: PJ Cardona
Funding agency: Fundació “la Caixa”
Agency code: LCF/PR/GN17/50300003
Duration: 2018 - 2022

Scientific publications

Highlighted publications

Russell DG, Cardona PJ, Kim MJ, Allain S, Altare F. Foamy macrophages and the progression of the human tuberculosis granuloma. Nat Immunol. 2009 Sep;10(9):943-8. DOI: 10.1038/ni.1781.

Marzo E, Vilaplana C, Tapia G, Diaz J, Garcia V, Cardona PJ. Damaging role of neutrophilic infiltration in a mouse model of progressive tuberculosis. Tuberculosis (Edinb). 2014 Jan;94(1):55-64. DOI: 10.1016/j.tube.2013.09.004.

Cardona PJ, Català M, Prats C. Origin of tuberculosis in the Paleolithic predicts unprecedented population growth and female resistance. Sci Rep. 2020 Jan 8;10(1):42. DOI: 10.1038/s41598-019-56769-1.

Garrido-Amaro C, Cardona P, Gassó D, Arias L, Velarde R, Tvarijonativiciute A, Serrano E, Cardona PJ. Protective Effect of Intestinal Helminthiasis Against Tuberculosis Progression Is Abrogated by Intermittent Food Deprivation. Front Immunol. 2021 Apr 14;12:627638. DOI: 10.3389/fimmu.2021.627638.

Wang-Wang JH, Bordoy AE, Martró E, Quesada MD, Pérez-Vázquez M, Guerrero-Murillo M, Tiburcio A, Navarro M, Castellà L, Sopena N, Casas I, Saludes V, Giménez M, Cardona PJ. Evaluation of Fourier Transform Infrared Spectroscopy as a First-Line Typing Tool for the Identification of Extended-Spectrum β-Lactamase-Producing Klebsiella pneumoniae Outbreaks in the Hospital Setting. Front Microbiol. 2022 Jun 9;13:897161. DOI: 10.3389/fmicb.2022.897161.


Additional information

Collaborative networks


CIBERES' mission is to fight respiratory diseases by fostering excellence in research and quickly and safely transferring this to clinical practice. Its objectives are:

  • To foster excellence in research in respiratory diseases.
  • To help solving healthcare problems in the field of respiratory diseases.
  • To foster its research groups' participation in international research activities, especially the ones included in European Framework R+D+i programmes.
  • To promote transfer of research results to society and in particular to the productive sector.
  • To train innovative and competitive researchers in respiratory diseases.
  • To make sure society learns about the main progress made in respiratory research.


Systems biology has already produced extraordinary insights in biological and clinical research problems. This is particularly true since high-throughput experimental and computational approaches became available. However, the application of systems biology approaches is not straightforward, it involves the combination of complex and large datasets, exceptional analytical challenges, and targeted experimental approaches. Such a wide range of required scientific expertise is unlikely to be reachable by a single group. This is especially true for non-model organisms for which many tools are lacking or not yet standardised.

MycoNET was initially funded by nine research groups working on mycobacterial research with seminal contributions in their disciplines. The current number of groups is 13. The groups include experts on key mycobacteria research areas like omics and computational approaches, targeted functional approaches, animal models, clinical and epidemiological research. UMCiE foresees the role of MycoNET as a key instrument to create a Spanish systems biology framework for mycobacteria. A series of actions are implemented to attract new scientists, complement the research expertise of the groups, generate scientific knowledge, standardise research approaches and foster current national and international projects led by the different members. A successful systems biology framework will likely lead to major advancements in a series of topics, including basic bacterial biology, bioremediation, clinical, epidemiological, drug and vaccine research.

Doctoral theses

Title: Patrons de progresió de la tuberculosi pulmonar en model experimental animal en macacos mitjançant l'avaluació per tomografía computada
Author: Isabel Nogueira Mañas
Co-director: Pere-Joan Cardona
Date of defense: 12 April 2023


El Centre de Medicina Comparativa i Bioimatge de Catalunya celebra el seu cinquè aniversari

El CMCiB va celebrar els seus primers cinc anys d'activitat en un simposi dedicat a la recerca biomèdica pionera al CosmoCaixa.

- Campus Can Ruti, , Divulgació

Es tanca un nou cicle de visites de La Marató als laboratoris de l'IGTP

Un cop més, el programa "Visita la recerca" de la Fundació La Marató de TV3 ha conclòs amb èxit a l'Institut de Recerca Germans Trias i Pujol (IGTP), on una vintena de col·laboradors han tingut l'oportunitat de descobrir de primera mà els projectes de recerca que reben suport a través d'aquesta iniciativa solidària. 

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