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.

Training

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

• 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.