A5047440120- Streptococcal Infections and Treatments
- Pneumonia and Respiratory Infections
- Antibiotic Resistance in Bacteria
- Bacteriophages and microbial interactions
- Antimicrobial Resistance in Staphylococcus
- SARS-CoV-2 and COVID-19 Research
- Immunodeficiency and Autoimmune Disorders
- Genomics and Phylogenetic Studies
- Interstitial Lung Diseases and Idiopathic Pulmonary Fibrosis
- Bacterial Identification and Susceptibility Testing
- Neonatal and Maternal Infections
- Infective Endocarditis Diagnosis and Management
- Antibiotics Pharmacokinetics and Efficacy
- COVID-19 Clinical Research Studies
- Mycobacterium research and diagnosis
- RNA and protein synthesis mechanisms
- Bacterial Genetics and Biotechnology
- Cystic Fibrosis Research Advances
- Evolution and Genetic Dynamics
- CAR-T cell therapy research
- Neutropenia and Cancer Infections
- Vibrio bacteria research studies
- Microbial infections and disease research
- Parvovirus B19 Infection Studies
- Enterobacteriaceae and Cronobacter Research
Bambino Gesù Children's Hospital
2022-2025
Istituti di Ricovero e Cura a Carattere Scientifico
2022-2025
University of Milan
2022-2025
University of Siena
2021-2023
Background Group A Streptococcus (GAS) causes multiple clinical manifestations, including invasive (iGAS) or even life-threatening (severe-iGAS) infections. After the drop in cases during COVID-19 pandemic, 2022 a sharp increase of GAS was reported globally. Methods strains collected 09/2022–03/2023 two university hospitals Milan, Italy were retrospectively analyzed. Clinical/epidemiological data combined with whole-genome sequencing to: (i) define resistome/virulome, (ii) identify putative...
Abstract Objectives Genomic surveillance of Klebsiella pneumoniae carbapenemase-producing (KPC-Kp) is crucial for virulence, drug-resistance monitoring, and outbreak containment. Methods analysis on 87 KPC-Kp strains isolated from 3 Northern Italy hospitals in 2019-2021 was performed by whole genome sequencing (WGS), to characterize resistome, virulome, mobilome, assess potential associations with phenotype resistance clinical presentation. Maximum Likelihood Minimum Spanning Trees were used...
Abstract Little is known about SARS-CoV-2 evolution under Molnupiravir and Paxlovid, the only antivirals approved for COVID-19 treatment. By investigating variability in 8 Molnupiravir-treated, 7 Paxlovid-treated 5 drug-naïve individuals at 4 time-points (Days 0-2-5-7), a higher genetic distance found pressure compared to Paxlovid no-drug (nucleotide-substitutions/site mean±Standard error: 18.7 × 10 −4 ± 2.1 vs. 3.3 0.8 3.1 , P = 0.0003), peaking between Day 2 5. drives emergence of more G-A...
COVID-19 has significantly affected hospital infection prevention and control (IPC) practices, especially in intensive care units (ICUs). This frequently caused dissemination of multidrug-resistant organisms (MDROs), including carbapenem-resistant Acinetobacter baumannii (CRAB). Here, we report the management a CRAB outbreak large ICU hub Hospital Italy, together with retrospective genotypic analysis by whole-genome sequencing (WGS). Bacterial strains obtained from severe mechanically...
Background: Bloodstream infections affect up to 20% of pediatric cancer patients receiving intensive care, contributing significantly morbidity and mortality, with infection-related mortality rates reported be as high 16%. Methods: The identification microorganisms directly from whole blood is difficult due several factors, such interference host genomic material, low bacterial load, the endogenous components exogenous substances, which can interfere process. Nevertheless, rapid microbial...
Background/Objectives: Paediatric osteoarticular infections (POAIs) present unique diagnostic and therapeutic challenges. Microbiological culture (MC) is typically time-consuming lacks sensitivity, especially when patients have received antibiotics. The BIOFIRE® Joint Infection Panel (BJIP) a syndromic molecular assay for the direct identification of most pathogens causing POAIs. Methods: We evaluated BJIP in 17 synovial fluids, then, we retrospectively assessed its utility 93 off-label...
Despite effective HIV suppression, neuroinflammation and neurocognitive issues are prevalent in people with (PWH) yet poorly understood. infection alters the human virome, virome perturbations have been linked to without HIV. Once thought be sterile, cerebrospinal fluid (CSF) hosts a recently discovered presenting an unexplored avenue for understanding brain mental health PWH. This cross-sectional study analyzed 85 CSF samples (74 from PWH on suppressive antiretroviral therapy, 11 controls...
Abstract Since its emergence, SARS-CoV-2 Omicron clade has shown a marked degree of variability and different clinical presentation compared with previous clades. Here we demonstrate that at least four lineages circulated in children since December 2021, studied until November 2022: BA.1 (33.6%), BA.2 (40.6%), BA.5 (23.7%) BQ.1 (2.1%). At 70% infections concerned under 1 year, most them being infected (n = 201, 75.6%). Looking genetic variability, 69 SNPs were found to be significantly...
Invasive group A streptococci infections are increasing worldwide, mainly due to the emm1 lineage M1 UK emergence. Although this variant has recently been described in adult Italian patients, its circulation children not yet established. Characterizing by whole genome sequencing 6 invasive strains isolated between 2022 and 2023, we highlighted pediatric patients Italy.
Bacteriophages play an important role in bacterial physiology and genome evolution. The widespread use of sequencing revealed that genomes can contain several different integrated temperate bacteriophages, which constitute up to 20% the genome.
Carbapenem resistant Klebsiella pneumoniae (cr-Kp) causes serious infections associated with a high mortality rate. The clinical efficacy of ceftazidime/avibactam (CZA), meropenem/vaborbactam (M/V), and imipenem/relebactam (I/R) against cr-Kp is challenged by the emergence strains, making investigation monitoring main resistance mechanisms crucial. In this study, we reported genome characterization strain isolated from critically ill patient characterized multidrug (MDR) profile, including...
The complete genome sequence of Streptococcus pneumoniae strain Rx1, a Hex mismatch repair-deficient standard transformation recipient, was obtained by combining Nanopore and Illumina sequencing technologies. consists 2.03-Mb circular chromosome, with 2,054 open reading frames GC content 39.72%.
Cystic fibrosis (CF) is a life-threatening genetic disease characterised by chronic lung infections sustained opportunistic pathogens such as
Background: Infant meningitis, particularly caused by Escherichia coli, remains a life-threatening condition, especially in premature and low-weight infants. Infections of the central nervous system can be fatal, necessitating prompt diagnosis appropriate treatment. Acute infections various pathogens, including E. often present with similar clinical symptoms. The rapid identification pathogens their antimicrobial resistance mechanisms is critical for timely effective We report case an...
DNA sequencing of whole bacterial genomes has revealed that the entire set mobile genes (mobilome) represents as much 25% genome. Despite huge availability sequence data, functional analysis genetic elements (MGEs) is rarely reported. Therefore, established laboratory protocols are needed to investigate biology this important part Conjugation a mechanism horizontal gene transfer which allows exchange MGEs among strains same or different species. In streptococci and enterococci, integrative...
In streptococci, the type M resistance to macrolides is due mef(A)-msr(D) efflux transport system of ATP-Binding cassette (ABC) superfamily, where it proposed that mef(A) codes for transmembrane channel and msr(D) two ATP-binding domains. Phage ϕ1207.3 Streptococcus pyogenes, carrying gene pair, able transfer macrolide phenotype pneumoniae. Deletion in pneumococcal ϕ1207.3-carrying strains did not affect erythromycin efflux. order identify candidate genes likely involved complementation...
Background: Whole-genome sequencing (WGS) provides important information for the characterization, surveillance, and monitoring of antimicrobial resistance (AMR) determinants, particularly in cases multi- extensively drug-resistant microorganisms. We reported results a WGS analysis carried out on carbapenemases-producing Klebsiella pneumoniae, which causes hospital-acquired infections (HAIs) is characterized by marked profile. Methods: Clinical, phenotypic, genotypic data were collected AMR...
Tn5253, a composite Integrative Conjugative Element (ICE) of Streptococcus pneumoniae carrying tet(M) and cat resistance determinants, was found to (i) integrate at specific 83-bp integration site (attB), (ii) produce circular forms joined by 84-bp sequence (attTn), (iii) restore the chromosomal site. The purpose this study is functionally characterize attB in S. strains with different genetic backgrounds other bacterial species, investigate presence Tn5253 into genomes.Analysis...
Abstract Background Since its emergence in November 2021, SARS-CoV-2 Omicron clade has quickly become dominant, due to increased transmissibility and immune evasion. Different sublineages are currently circulating, which differ mutations deletions regions of the genome implicated response. In May 2022, BA.1 BA.2 were most prevalent Europe, both characterized by ability evading natural acquired vaccine-induced immunity escaping monoclonal antibodies neutralization. Case presentation A 5-years...
The whole-genome sequences of Mycobacterium chimaera strains 850 and 852, which were isolated from two different water samples obtained a heater-cooler unit at Siena University Hospital (Italy), determined by combining Nanopore Illumina technologies. Genomes both 852 consist circular chromosome five plasmids, with sizes 6,275,686 bp 6,453,144 bp, respectively.
Abstract Molnupiravir and Paxlovid are the only antivirals approved for COVID-19 treatment. Previous studies have evaluated their efficacy, tolerability, viral clearance, but little is known about SARS-CoV-2 evolution under pressure. Here dynamics of genomic in 8 Molnupiravir-treated, 7 Paxlovid-treated 5 drug-naïve individuals at 4 time-points (Day 0, Day 2, treatment 7) were in-depth investigated. strains pressure characterized by a higher genetic diversity compared to no-drug (mean ± SE:...
Disbalancing envelope stress responses was investigated as a strategy for sensitization of Escherichia coli to antimicrobial agents. Seventeen isogenic strains were selected from the KEIO collection with deletions in genes corresponding σ E , Cpx, Rcs, Bae, and Psp responses. Antimicrobial activity against 20 drugs different targets evaluated by disk diffusion gradient strip tests. Growth curves time-kill also determined mutant-antimicrobial combinations. An increase susceptibility...
Bacterial SOS response is an inducible system of DNA repair and mutagenesis. Streptococci lack a canonical response, but SOS-like was reported in some species. The mef(A)-msr(D)-carrying prophage Ф1207.3 Streptococcus pyogenes contains region, spanning orf6 to orf11, showing homology characterized streptococcal cassettes. Genome-wide search showed the presence whole Φ1207.3 cassette three S. prophages, while parts it were found other bacterial To investigate whether this confers...