31 Mar 2025

The LTTA Laboratory (Laboratory for Advanced Therapy Technologies) at the Technopole of Ferrara is a center of excellence with expertise ranging from life sciences to medicine and biotechnology. The Clinical Research unit is one of its research areas, in which the group led by Elisabetta Caselli from the Department of Environmental and Prevention Sciences operates. This group is specialized in microbiological monitoring and the analysis of the bacterial resistome using a technique based on microarray via quantitative real-time PCR. We asked Elisabetta Caselli a few questions to better understand her work.

What is meant by the term antimicrobial resistance (AMR)?

Antimicrobial resistance (AMR) refers to the ability of a microorganism to survive and proliferate in the presence of an antimicrobial agents that were previously capable of inhibiting or killing it. In recent decades, the inappropriate and excessive use of antibiotics led to the emergence and spread of AMR in many pathogenic microorganisms, making infections increasingly difficult to treat and often fatal.

AMR has recently been identified as one of the three most urgent threats to global public health, causing more than 35,000 deaths per year in Europe alone, with a significant increase in healthcare costs. The hospital environment is particularly affected by this issue, as the high use of antimicrobial drugs and disinfectants exerts constant selective pressure on the microbiota that persistently colonizes hospital environments. This contributes to the spread of bacteria resistant to multiple antibiotics (MDR, multi-drug resistant) or even to all available antibiotics (PDR, pan-drug resistant, also defined TDR, totally drug-resistant), which are often responsible for the onset of the so-called healthcare-associated infections (HAIs). However, the spread of AMR is not limited to healthcare settings but also extends to community environments (offices, schools, public transport), households, agriculture, and veterinary sectors.

Why is it important to monitor AMR?

Monitoring drug resistance is essential to control and limit its spread, in accordance with the "One Health" principles promoted by the World Health Organization. In many contexts, there is an urgent need to rapidly and accurately monitor the microbial population colonizing a given environment (microbiome) and the associated resistance genes (resistome).

For this purpose, conventional microbiological methods, such as antibiograms, based on cultural isolation of target microorganisms, have significant limitations, including long processing time and results limited to isolated species. Conversely, molecular methods based on the analysis of genetic material offer greater speed, sensitivity, and specificity. Genetic targeted amplification techniques (PCR) allow for the detection and quantification of even traces of targets within a few hours and can be applied to the entire microbial population.

What technique have you developed for monitoring AMR?

For over ten years, our group has developed an analysis method based on microarray via quantitative real-time PCR (qPCR microarray) for detecting drug resistance genes. This technique allows the simultaneous identification and quantification of 84 resistance genes in each sample and in a single PCR cycle performed in 96-well plates, covering various antibiotic categories such as beta-lactams, macrolides, quinolones, and tetracyclines.

This approach enables a targeted analysis of the most relevant resistance genes within a few hours, with high sensitivity, speed, and specificity. Moreover, it keeps analysis time and costs lower than high-throughput sequencing methods (NGS, WGS). This methodology is applicable not only to human clinical samples but also to environmental, animal, and plant samples.

In what contexts has this method been applied?

Our method has been successfully used to characterize the bacterial resistome in numerous contexts, including clinical samples (oral microbiome), environmental samples (sand from bathing beaches), community settings (Milan subway, public schools in Ferrara), healthcare environments (internal medicine hospital wards, neonatal intensive care units, emergency rooms of various Italian hospitals), and veterinary settings (poultry farms).

The results obtained have published in peer-reviewed international scientific journals and have inspired numerous research projects in collaboration with other groups, demonstrating their high utility as a tool for understanding the spread of antibiotic resistance and its implications for public health.