Exploring Hospital and Patient Microbiomes for Advanced Nano-detectors Development and Antibiotic Resistance Monitoring

Humans are constantly exposed to environmental microbes through contact with surfaces, air, water and food. Likewise, people scatter microbes through skin, saliva and feces, contributing to the interconnection between micro- and macro-organisms. Particularly, hospitals, clinics, and other healthcare facilities are environments of specific interest due to treatment-derived infections and the increasing antimicrobial resistance (AMR) outbreak. These have both arisen as two primary public health challenges in this century, approximately, 4.95 million deaths were associated with bacterial AMR globally in 2019 and W.H.O. estimated that 15% of hospitalised patients suffered from nosocomial infections in 2023. Regarding healthcare-associated infections, their causes can be multiple, such as invasive medical procedures that introduce opportunistic bacteria into the body, contaminated medical equipment and overcrowding that increases the risk of person-to-person transmission of infectious agents. Moreover, healthcare facilities can harbour pathogens that are transmitted via contaminated surfaces, air vents and water systems if not properly cleaned and maintained. Actual standard diagnostic methods are expensive, require trained personnel and a significant time investment, making early diagnosis difficult. Patients with nosocomial infections are more prone to be infected with multidrug-resistant bacteria, making treatment more difficult. Hospitals are environments of strong artificial selection on microbial communities. The over-cleaning methods and the overuse and misuse of antibiotics and antimicrobials drive the antimicrobial resistance spread and contribute to developing a unique built environment microbiota. As part of the ANTHEM project, the presented study aims to characterise the hospital’s microbiome and to reduce and monitor the spread of AMR bacteria and antibiotic resistance genes in hospital settings. Based on our microbiome characterization, the long-term aim of the project is to build fast and easy-to-use technological devices grounded on biomolecular techniques. To address these issues, we plan to combine biomolecular and bioinformatics approaches consisting of data from public repositories and newly generated data collected from patients, and from different environmental sites of the pre-admission ward and intensive care unit at different times of the day. In particular, by characterising hospital microbial communities with DNA sequencing, we will define a set of pathogens that are easily shared between patients and the environment that will be used to develop rapid and user-friendly nanosensors for microbial detection. At the same time, we will define local environmental features that induce the spread of AMR to define new strategies and policies to promote more conscious antibiotic use and drive bio-informed cleaning techniques. In conclusion, our project will help in reducing nosocomial infections and fighting AMR spread in patients, healthcare workers and the general population by restoring a healthier relationship between humans and their microbial communities.