Molecular methods and bioinformatics - IM
The research projects focus on the development of classical microbiological methods, such as isolation, cultivation, and the execution of tests to highlight specific phenotypic characteristics, molecular biology methods, particularly those based on PCR (amplification of specific DNA regions) and sequencing, and proteomics, i.e., the identification and characterization of proteins, to obtain the "fingerprints" of microorganisms. These fingerprints are necessary to identify, i.e., give a name to, and/or typing, i.e., distinguish, an unknown microorganism or one with specific metabolic capabilities. Fingerprinting methods are applied in various fields for the characterization of microorganisms, epidemiology and molecular epidemiology, environmental monitoring, and the study of the dynamics of natural microbial populations.
In recent years, we have implemented next-generation sequencing (NGS) as an innovative and highly versatile technology that allows parallel sequencing of millions of DNA fragments.
This technique, based on Illumina's iSEQ100 and Oxford Nanopore Technologies' MinION instruments, enables the study of the nucleotide composition of an entire microorganism's genome (Whole-genome sequencing - WGS), or the identification of all members of a microbial community, including unculturable and rare species (metagenomics). These approaches allow us to establish the degree of (bio)diversity of microbial communities residing in different matrices and environments and to study the relationships between microorganisms that are part of the same community, whether they are residents or contaminants. In parallel, the sector is acquiring and developing the necessary IT infrastructure for managing and analyzing NGS data, guided by a professional specializing in bioinformatics.
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Innovations in microbiological diagnostics
The application of MALDI-TOF mass spectrometry for the identification and typing of microorganisms, which was introduced in Ticino in 2008 by the then Cantonal Institute of Microbiology as the first microbiological diagnostic institute in Switzerland, represents a specific competency that positions the Institute of Microbiology as a service laboratory for SUPSI and externals. The IM database is continuously expanding and currently enables rapid and accurate identification of environmental bacteria, pathogenic bacteria, filamentous fungi, and mosquitoes.
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Current Methodologies
The methodologies currently at the forefront in this sector are mass spectrometry (MALDI-TOF MS) and next-generation sequencing (NGS).