A5011092050- Genomics and Phylogenetic Studies
- Antibiotic Resistance in Bacteria
- Veterinary medicine and infectious diseases
- Parasitic Infections and Diagnostics
- Clostridium difficile and Clostridium perfringens research
- Plant Pathogenic Bacteria Studies
- Protein Structure and Dynamics
- Antibiotics Pharmacokinetics and Efficacy
- Probiotics and Fermented Foods
- Antibiotic Use and Resistance
- Enzyme Structure and Function
- Insect symbiosis and bacterial influences
- Pharmaceutical and Antibiotic Environmental Impacts
- Vector-borne infectious diseases
- Bacteriophages and microbial interactions
- Oral Health Pathology and Treatment
- Microbial Metabolic Engineering and Bioproduction
- Insect and Pesticide Research
- Vibrio bacteria research studies
- Infections and bacterial resistance
- Cell Image Analysis Techniques
- Advanced Proteomics Techniques and Applications
- Bacterial Identification and Susceptibility Testing
- Gut microbiota and health
- Genetic diversity and population structure
University of Pavia
2022-2024
The order Rickettsiales (Alphaproteobacteria) encompasses multiple diverse lineages of host-associated bacteria, including pathogens, reproductive manipulators, and mutualists. Here, in to understand how intracellularity host association originated this order, whether they are ancestral or convergently evolved characteristics, we built a large phylogenetically-balanced dataset that includes de novo sequenced genomes selection published genomic metagenomic assemblies. We perform detailed...
Abstract Summary Bacterial Healthcare-Associated Infections (HAIs) are a major threat worldwide, which can be counteracted by establishing effective infection control measures, guided constant surveillance and timely epidemiological investigations. Genomics is crucial in modern epidemiology but lacks standard methods user-friendly software, accessible to users without strong bioinformatics proficiency. To overcome these issues we developed P-DOR, novel tool for rapid bacterial outbreak...
Abstract Motivation Discovering new protein–protein interactions (PPIs) across entire proteomes offers vast potential for understanding novel protein functions and elucidate system properties within or between an organism. While recent advances in computational structural biology, particularly AlphaFold-Multimer, have facilitated this task, scaling large-scale screenings remains a challenge, requiring significant resources. Results We evaluated the impact of reducing number models generated...
Acinetobacter baumannii is a nosocomial pathogen that poses serious threat due to the rise of incidence multidrug-resistant (MDR) strains. During COVID-19 pandemic, MDR A. clones have caused several outbreaks worldwide. Here, we describe detailed investigation an outbreak occurred at Policlinico San Matteo (Pavia, Italy). A total 96 strains, isolated between January and July 2020 from 41 inpatients (both SARS-CoV-2 positive negative) in different wards, were characterized by phenotypic...
The zoonotic parasite
ABSTRACT Yeasts belonging to the Candida genus typically reside on mucosal surface and within respiratory gastrointestinal tract as commensals. Under conditions of host vulnerability, they can act opportunistic pathogens, leading various forms candidiasis, including candidemia. Such infections be particularly problematic when caused by isolates that exhibit resistance antifungal drugs, which is becoming more prevalent in many regions. One hundred seven samples spp. were isolated from...
Abstract The order Rickettsiales ( Alphaproteobacteria ) encompasses multiple diverse lineages of host-associated bacteria, including pathogens, reproductive manipulators, and mutualists. In to understand how intracellularity host association originated in this order, whether they are ancestral or convergently evolved characteristics, we built an unprecedentedly large phylogenetically-balanced dataset that includes de novo sequenced genomes accurate selection published genomic metagenomic...
Abstract Genome plasticity can be defined as the capacity of a bacterial population to swiftly gain or lose genes. The time factor plays fundamental role for evolutionary success microbes, particularly when considering pathogens and their tendency antimicrobial resistance factors under pressure extensive use antibiotics. Multiple metrics have been proposed provide insights into gene content repertoire, yet they overlook temporal component, which has critical in determining adaptation...
Abstract Motivation Discovering new protein-protein interactions (PPIs) across entire proteomes offers vast potential for understanding novel protein functions and elucidate system properties within or between an organism. While recent advances in computational structural biology, particularly AlphaFold-Multimer, have facilitated this task, scaling large-scale screenings remains a challenge, requiring significant resources. Results Here we introduce AlphaFastPPi, pipeline built upon...
Ticks are prominent vectors of several zoonotic diseases. Tick-borne pathogens include the members genus Ehrlichia, which obligate intracellular bacteria infecting immune and hematopoietic cells. Ehrlichia muris predominantly affects rodents, but was also reported to be a human pathogen. The known geographical distribution this bacterium ranges from Asia, USA eastern Europe. In present work, we report finding E. in an Ixodes ricinus tick collected migratory bird (Turdus iliacus) Italy,...
Summary Bacterial Healthcare Associated Infections (HAIs) are a major threat worldwide, which can be counteracted by establishing effective infection control measures, guided constant surveillance and timely epidemiological investigations. Genomics is crucial in modern epidemiology but lacks standard methods user-friendly software, accessible to users without strong bioinformatics proficiency. To overcome these issues we developed P-DOR, novel tool for rapid bacterial outbreak...
In this study, we present two cases of
Abstract The zoonotic parasite Cryptosporidium parvum is a global cause of gastrointestinal disease in humans and ruminants. Sequence analysis the highly polymorphic gp60 gene enabled classification C. isolates into multiple groups (e.g. IIa, IIc, Id) large number subtypes. In Europe, subtype IIaA15G2R1 largely predominant has been associated with many water-and food-borne outbreaks. this study, we generated new whole genome sequence (WGS) data from 123 human-and ruminant-derived collected...
Abstract Acinetobacter baumannii is a nosocomial pathogen that poses serious threat due to the rise of incidence multidrug resistant (MDR) strains. During COVID-19 pandemic, MDR A.baumannii clones have caused several outbreaks worldwide. Here we describe detailed investigation an A. outbreak occurred at Fondazione IRCCS Policlinico San Matteo (Pavia, Italy). A total 96 strains, isolated between January and July 2020 from 41 inpatients (both SARS-CoV-2 positive negative) in different wards,...