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View article: Whole-Genome Sequencing of Adenovirus Genotypes and Clinical Implications in Pediatric Patients
Whole-Genome Sequencing of Adenovirus Genotypes and Clinical Implications in Pediatric Patients Open
Human adenoviruses (HAdV) comprise more than 100 genotypes with species-specific differences in tropism and immune response and can cause severe infections in immunocompromised patients. This study aimed to characterise the HAdV species in…
View article: The cerebrospinal fluid virome in people with HIV: links to neuroinflammation and cognition
The cerebrospinal fluid virome in people with HIV: links to neuroinflammation and cognition Open
Introduction Despite durable viral suppression, neuroinflammation and neurocognitive complications remain common yet poorly understood in people with HIV (PWH). HIV alters human viromes, and virome perturbations have been linked to neuroco…
View article: When Conventional Methods Fail: First Detection of a <i>Candida viswanathii</i> Outbreak in Europe in a Paediatric Hospital Revealed by Whole Genome Sequencing and FT-IR Spectroscopy
When Conventional Methods Fail: First Detection of a <i>Candida viswanathii</i> Outbreak in Europe in a Paediatric Hospital Revealed by Whole Genome Sequencing and FT-IR Spectroscopy Open
Objectives Candida viswanathii has been sporadically reported in Asia and South America but never in Europe. This study reports the first European outbreak of C. viswanathii in a paediatric hospital, outlining diagnostic challenges and con…
View article: Clinical manifestations and severity of COVID-19 caused by Omicron among paediatric patients aged 0–17 years in Italy
Clinical manifestations and severity of COVID-19 caused by Omicron among paediatric patients aged 0–17 years in Italy Open
View article: Killing two birds with one stone: emergence of colistin and cefiderocol resistance in a mucoid MDR Acinetobacter baumannii under colistin pressure
Killing two birds with one stone: emergence of colistin and cefiderocol resistance in a mucoid MDR Acinetobacter baumannii under colistin pressure Open
Acinetobacter baumannii is a multidrug-resistant (MDR) pathogen associated with nosocomial infections, sporadically detected in cystic fibrosis (CF) patients. Treatment of A. baumannii may be hindered by polysaccharide capsule production o…
View article: Potential role of avibactam in restoring susceptibility in Escherichia coli with two copies of blaKPC-3 and PBP3 mutations
Potential role of avibactam in restoring susceptibility in Escherichia coli with two copies of blaKPC-3 and PBP3 mutations Open
View article: Clinical relevance of bacterial and/or viral coinfection in acute bronchiolitis in an Italian neonatal unit during the 2021–2023 seasons
Clinical relevance of bacterial and/or viral coinfection in acute bronchiolitis in an Italian neonatal unit during the 2021–2023 seasons Open
Background Acute bronchiolitis is a leading cause of hospitalization in young children worldwide, and literature reports conflicting data regarding the role of coinfections. Objective To evaluate the possible clinical relevance of bacteria…
View article: Parvovirus B19 Rebound
Parvovirus B19 Rebound Open
Human parvovirus B19 (B19V) is responsible for a wide clinical spectrum ranging from asymptomatic infection, through mild disease, up to life‐threatening one. Outbreaks are registered every 3–4 years, and a recent international alert for a…
View article: The cerebrospinal fluid virome in people with HIV: links to neuroinflammation and cognition
The cerebrospinal fluid virome in people with HIV: links to neuroinflammation and cognition Open
Despite effective HIV suppression, neuroinflammation and neurocognitive issues are prevalent in people with HIV (PWH) yet poorly understood. HIV infection alters the human virome, and virome perturbations have been linked to neurocognitive…
View article: An Evaluation of a Syndromic Molecular Panel in Optimising the Microbiological Diagnosis and Antimicrobial Therapy of Suspected Osteoarticular Infections in Paediatric Patients
An Evaluation of a Syndromic Molecular Panel in Optimising the Microbiological Diagnosis and Antimicrobial Therapy of Suspected Osteoarticular Infections in Paediatric Patients Open
Background/Objectives: Paediatric osteoarticular infections (POAIs) present unique diagnostic and therapeutic challenges. Microbiological culture (MC) is typically time-consuming and lacks sensitivity, especially when patients have receive…
View article: The First Case of the Identification of a Microorganism Directly from Whole Blood Using MALDI-TOF Mass Spectrometry in an Onco-Hematological Pediatric Patient with Bloodstream Infection
The First Case of the Identification of a Microorganism Directly from Whole Blood Using MALDI-TOF Mass Spectrometry in an Onco-Hematological Pediatric Patient with Bloodstream Infection Open
Background: Bloodstream infections affect up to 20% of pediatric cancer patients receiving intensive care, contributing significantly to morbidity and mortality, with infection-related mortality rates reported to be as high as 16%. Methods…
View article: A case of Ustilago spp. infection identified by whole genome sequencing in a pediatric patient undergoing open-chest extracorporeal membrane oxygenation
A case of Ustilago spp. infection identified by whole genome sequencing in a pediatric patient undergoing open-chest extracorporeal membrane oxygenation Open
To the best of our knowledge, we presented the first case of an Ustilago spp infection in a pediatric patient undergoing ECMO, not identified by standard techniques but only by WGS performed directly on a blood sample in 5 days. Despite th…
View article: Integrating Diagnostic Approaches in Infant Bacterial Meningitis Caused by a Non-K1 Escherichia coli: A Case Report
Integrating Diagnostic Approaches in Infant Bacterial Meningitis Caused by a Non-K1 Escherichia coli: A Case Report Open
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 diagn…
View article: The Challenging Life of Mutators: How Pseudomonas aeruginosa Survives between Persistence and Evolution in Cystic Fibrosis Lung
The Challenging Life of Mutators: How Pseudomonas aeruginosa Survives between Persistence and Evolution in Cystic Fibrosis Lung Open
Cystic fibrosis (CF) is a life-threatening genetic disease characterised by chronic lung infections sustained by opportunistic pathogens such as Pseudomonas aeruginosa. During the chronic long-lasting lung infections, P. aeruginosa adapts …
View article: First Evidence of Streptococcus pyogenes M1UK Clone in Pediatric Invasive Infections in Italy by Molecular Surveillance
First Evidence of Streptococcus pyogenes M1UK Clone in Pediatric Invasive Infections in Italy by Molecular Surveillance Open
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 in children has not yet been es…
View article: Genomic characterization of Klebsiella pneumoniae carbapenemase-producing Klebsiella pneumoniae (KPC-Kp) strains circulating in three university hospitals in Northern Italy over three years
Genomic characterization of Klebsiella pneumoniae carbapenemase-producing Klebsiella pneumoniae (KPC-Kp) strains circulating in three university hospitals in Northern Italy over three years Open
Objectives Genomic surveillance of Klebsiella pneumoniae carbapenemase-producing Klebsiella pneumoniae (KPC-Kp) is crucial for virulence, drug-resistance monitoring, and outbreak containment. Methods Genomic analysis on 87 KPC-Kp strains i…
View article: Molecular characterization of SARS-CoV-2 Omicron clade and clinical presentation in children
Molecular characterization of SARS-CoV-2 Omicron clade and clinical presentation in children Open
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 Omicron lineages circulated in children since …
View article: Increase in invasive group A streptococcal infections in Milan, Italy: a genomic and clinical characterization
Increase in invasive group A streptococcal infections in Milan, Italy: a genomic and clinical characterization Open
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, in 2022 a sharp increase of GAS …
View article: A Whole-Genome Sequencing-Based Approach for the Characterization of Klebsiella pneumoniae Co-Producing KPC and OXA-48-like Carbapenemases Circulating in Sardinia, Italy
A Whole-Genome Sequencing-Based Approach for the Characterization of Klebsiella pneumoniae Co-Producing KPC and OXA-48-like Carbapenemases Circulating in Sardinia, Italy Open
Background: Whole-genome sequencing (WGS) provides important information for the characterization, surveillance, and monitoring of antimicrobial resistance (AMR) determinants, particularly in cases of multi- and extensively drug-resistant …
View article: The <i>mef</i> (A)/ <i>msr</i> (D)-carrying streptococcal prophage Φ1207.3 encodes an SOS-like system, induced by UV-C light, responsible for increased survival and increased mutation rate
The <i>mef</i> (A)/ <i>msr</i> (D)-carrying streptococcal prophage Φ1207.3 encodes an SOS-like system, induced by UV-C light, responsible for increased survival and increased mutation rate Open
Bacterial SOS response is an inducible system of DNA repair and mutagenesis. Streptococci lack a canonical SOS response, but an SOS-like response was reported in some species. The mef (A)- msr (D)-carrying prophage Ф1207.3 of Streptococcus…
View article: Genomic Characterization of Carbapenem-Resistant Acinetobacter baumannii (CRAB) in Mechanically Ventilated COVID-19 Patients and Impact of Infection Control Measures on Reducing CRAB Circulation during the Second Wave of the SARS-CoV-2 Pandemic in Milan, Italy
Genomic Characterization of Carbapenem-Resistant Acinetobacter baumannii (CRAB) in Mechanically Ventilated COVID-19 Patients and Impact of Infection Control Measures on Reducing CRAB Circulation during the Second Wave of the SARS-CoV-2 Pandemic in Milan, Italy Open
Infection prevention and control (IPC) practices are of paramount importance for preventing the spread of multidrug-resistant organisms (MDROs) in hospitals, especially in the intensive care unit (ICU). Whole-genome sequencing (WGS) is see…
View article: A case of SARS-CoV-2 Omicron reinfection resulting in a significant immunity boost in a paediatric patient affected by B-cell acute lymphoblastic leukemia
A case of SARS-CoV-2 Omicron reinfection resulting in a significant immunity boost in a paediatric patient affected by B-cell acute lymphoblastic leukemia Open
View article: Streptococcus pyogenes Φ1207.3 Is a Temperate Bacteriophage Carrying the Macrolide Resistance Gene Pair <i>mef</i> (A)- <i>msr</i> (D) and Capable of Lysogenizing Different Streptococci
Streptococcus pyogenes Φ1207.3 Is a Temperate Bacteriophage Carrying the Macrolide Resistance Gene Pair <i>mef</i> (A)- <i>msr</i> (D) and Capable of Lysogenizing Different Streptococci Open
Bacteriophages play an important role in bacterial physiology and genome evolution. The widespread use of genome sequencing revealed that bacterial genomes can contain several different integrated temperate bacteriophages, which can consti…
View article: Genomic Characterization of KPC-31 and OXA-181 Klebsiella pneumoniae Resistant to New Generation of β-Lactam/β-Lactamase Inhibitor Combinations
Genomic Characterization of KPC-31 and OXA-181 Klebsiella pneumoniae Resistant to New Generation of β-Lactam/β-Lactamase Inhibitor Combinations Open
Background: 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…
View article: A proof-of-concept study on the genomic evolution of Sars-Cov-2 in molnupiravir-treated, paxlovid-treated and drug-naïve patients
A proof-of-concept study on the genomic evolution of Sars-Cov-2 in molnupiravir-treated, paxlovid-treated and drug-naïve patients Open
View article: <i>Streptococcus pyogenes</i>ϕ1207.3 is a temperate bacteriophage carrying the macrolide efflux gene pair<i>mef</i>(A)-<i>msr</i>(D) and capable to lysogenise different Streptococci
<i>Streptococcus pyogenes</i>ϕ1207.3 is a temperate bacteriophage carrying the macrolide efflux gene pair<i>mef</i>(A)-<i>msr</i>(D) and capable to lysogenise different Streptococci Open
Streptococcus pyogenes prophage ϕ1207.3 (formerly Tn 1207.3 ) carries the mef (A)- msr (D) efflux resistance genes, responsible for type M macrolide resistance. To investigate if ϕ1207.3 is a functional bacteriophage, we transferred the el…
View article: Genomic Evolution of Sars-Cov-2 in Molnupiravir-Treated Patients Compared to Paxlovid-Treated and Drug-Naïve Patients: A Proof-of-Concept Study
Genomic Evolution of Sars-Cov-2 in Molnupiravir-Treated Patients Compared to Paxlovid-Treated and Drug-Naïve Patients: A Proof-of-Concept Study Open
Molnupiravir and Paxlovid are the only antivirals approved for COVID-19 treatment. Previous studies have evaluated their efficacy, tolerability, and viral clearance, but little is known about SARS-CoV-2 evolution under their pressure. Here…
View article: Complete Genome Sequences of Mycobacterium chimaera Strains 850 and 852, Isolated from Heater-Cooler Unit Water
Complete Genome Sequences of Mycobacterium chimaera Strains 850 and 852, Isolated from Heater-Cooler Unit Water Open
The whole-genome sequences of Mycobacterium chimera strains 850 and 852, which were isolated from two different water samples obtained from a heater-cooler unit at Siena Hospital (Italy), were determined by combining Nanopore and Illumina …
View article: Predicted transmembrane proteins with homology to Mef(A) are not responsible for complementing mef(A) deletion in the mef(A)–msr(D) macrolide efflux system in Streptococcus pneumoniae
Predicted transmembrane proteins with homology to Mef(A) are not responsible for complementing mef(A) deletion in the mef(A)–msr(D) macrolide efflux system in Streptococcus pneumoniae Open
View article: Chromosomal integration of Tn5253 occurs downstream of a conserved 11-bp sequence of the rbgA gene in Streptococcus pneumoniae and in all the other known hosts of this integrative conjugative element (ICE)
Chromosomal integration of Tn5253 occurs downstream of a conserved 11-bp sequence of the rbgA gene in Streptococcus pneumoniae and in all the other known hosts of this integrative conjugative element (ICE) Open