Microbiology, Immunology and Microbiology, Applied Microbiology and Biotechnology
31
Scopus Publications
Scopus Publications
Clonal lineage and biofilm growth shape cefiderocol activity in Acinetobacter baumannii from oncology patients Ilaria Cavallo, Francesca Sivori, Mauro Truglio, Massimo Francalancia, Elva Abril, Giorgia Fabrizio, Sara Petrolo, Francesca Maione, Grazia Prignano, Arianna Mastrofrancesco, Fulvia Pimpinelli, Enea Gino Di Domenico Frontiers in Cellular and Infection Microbiology, 2026 Introduction Acinetobacter baumannii is a leading cause of healthcare-associated infections in immunocompromised patients and frequently exhibits multidrug resistance. Cefiderocol, a siderophore cephalosporin, is among the few remaining therapeutic options for infections caused by carbapenem-resistant A. baumannii (CRAB); however, its activity may differ by clonal lineage and can be further compromised in the biofilm state. This study investigates genomic features and cefiderocol efficacy against planktonic and biofilm-associated forms of oncology-derived A. baumannii isolates. Methods Twenty-five non-duplicate, consecutive clinical isolates of A. baumannii from oncology patients underwent whole-genome sequencing and multilocus sequence typing. Cefiderocol activity was quantified in planktonic and biofilm-associated states using minimum bactericidal concentration (MBC) and minimum biofilm eradication concentration (MBEC) assays. Results Ten sequence types were identified, with the high-risk sequence type 2 (ST2) clone accounting for 56% (14/25) of isolates. ST2 strains showed significantly higher resistance to aminoglycosides, carbapenems, and fluoroquinolones than non-ST2 (NST) strains. The carbapenemase gene bla OXA−23 was detected exclusively in ST2. Colistin and cefiderocol were the most active agents overall. ST2 strains showed higher cefiderocol MBC values than NST strains. However, avibactam significantly reduced cefiderocol MBC in ST2, consistent with class D β-lactamases activity. ST2 and NST isolates exhibited comparable distributions of iron acquisition genes and similar CAS-detected siderophore activity under the assay conditions tested. Cefiderocol activity was significantly reduced in biofilms relative to planktonic cells (median MBEC 2 µg/ml versus median MBC 0.5 µg/ml). NST exhibited higher MBEC/MBC ratios than ST2 isolates, indicating greater biofilm-associated tolerance to cefiderocol. Discussion Collectively, these data associate the predominance of oncology-derived ST2 with bla OXA-23 carriage and higher cefiderocol bactericidal thresholds and show that cefiderocol activity is consistently reduced in the biofilm state. Future studies integrating functional measures of iron acquisition and β-lactamase activity will be needed to define the determinants of cefiderocol efficacy across lineages and growth states.
Cefiderocol activity against planktonic and biofilm forms of β-lactamase-producing pseudomonas aeruginosa from people with cystic fibrosis Giorgia Fabrizio, Mauro Truglio, Ilaria Cavallo, Francesca Sivori, Massimo Francalancia, Rodolfo J. Riveros Cabral, Manola Comar, Maria Trancassini, Daniele Emanuele Compagnino, Fabiana Diaco, Guido Antonelli, Fiorentina Ascenzioni, Giuseppe Cimino, Fulvia Pimpinelli, Enea Gino Di Domenico Journal of Global Antimicrobial Resistance, 2025 • Whole genome sequencing revealed significant variability in β-lactamases among isolates. • Resistance to cefiderocol was linked to the blaOXA486 gene and iron uptake defects. • Combining cefiderocol with avibactam restored susceptibility in β-lactamase-producing strains. • Biofilm formation increased cefiderocol tolerance by 8-fold compared to planktonic cells. Objectives: Chronic Pseudomonas aeruginosa infections are a leading cause of acute pulmonary exacerbations in people with cystic fibrosis (pwCF). Intrinsic antibiotic resistance and biofilm formation complicate treatment. This study investigates the genomic diversity and cefiderocol efficacy against planktonic and biofilm-associated forms of P. aeruginosa isolates from pwCF. Methods: Eight P. aeruginosa clinical isolates and three laboratory strains underwent whole genome sequencing (WGS). Biofilm formation was assessed through biomass, cell count, metabolic activity, and extracellular DNA (eDNA). The minimum bactericidal concentration (MBC 90 ) and biofilm eradication concentration (MBEC 90 ) were also determined. Results: WGS revealed significant genomic diversity, identifying ten distinct sequence types (STs). Antibiotic susceptibility testing (AST) showed that 10/11 strains were susceptible to cefiderocol, with one isolate (MPA9) displaying resistance linked to the bla OXA486 gene. Adding the β-lactamase inhibitor avibactam (AVI) restored susceptibility in this resistant strain. Although iron metabolism genes were highly conserved across isolates, MPA9 lacked the fpvA iron receptor, potentially contributing to cefiderocol resistance. Biofilm formation significantly increased tolerance to cefiderocol, with an 8-fold rise in MBEC 90 compared to MBC 90 . Conclusion: These findings highlight the genomic diversity and adaptive potential of P. aeruginosa in pwCF. Cefiderocol shows promise against planktonic and biofilm-associated P. aeruginosa , and combining it with AVI may counteract β-lactamase-mediated resistance.
Virulence profile of carbapenem-resistant Klebsiella pneumoniae strains by an in vivo model of Galleria mellonella María Guembe, Rama Hafian, Marta Díaz-Navarro, Andrés Visedo, Flavio De Maio, Fulvia Pimpinelli, Ilaria Cavallo, Mauro Truglio, Francesca Sivori, Enea Gino Di Domenico Microbiology Spectrum, 2025 Klebsiella pneumoniae is a significant healthcare-associated pathogen, notable for its diverse virulence and antibiotic resistance profiles. This study aimed to characterize the genotypic and phenotypic diversity of K. pneumoniae isolates and evaluate their virulence using the Galleria mellonella model. Biomass production, metabolic activity, capsule formation, and siderophore production were assessed in 27 K . pneumoniae isolates from hospital-associated infections. Lethality curves were generated using the G. mellonella model, with survival monitored hourly from 16 to 48 hours. The most common sequence types (ST) identified were the high-risk clones ST307 ( N = 10), ST512 ( N = 8), ST101 ( N = 7), and ST661 ( N = 2). These STs were associated with distinct K-locus, including KL102, KL107, KL17, and KL39. Most isolates belonged to the O2afg locus ( N = 18), with the K. pneumoniae carbapenemase genotype detected in 96.3% of strains. None of the isolates were classified as hypervirulent. Phenotypically, ST661 exhibited the highest biomass production despite showing similar metabolic activity to other STs. A positive correlation was observed between biomass and siderophore production, while capsule production was inversely correlated with biomass. In the G. mellonella model, ST661 demonstrated the highest virulence, resulting in 100% mortality by 48 hours, compared to survival rates of 21.4% for ST101, 38.0% for ST307, and 31.2% for ST512. These findings underscore the pathogenic potential of ST661 isolates with enhanced biofilm production. The G. mellonella model may serve as an effective in vivo system for evaluating the virulence of emerging K. pneumoniae lineages. IMPORTANCE We demonstrate that the Galleria mellonella model is a useful tool to analyze the virulence of carbapenem-resistant Klebsiella pneumoniae strains. Our findings highlight the pathogenicity of carbapenem-resistant K pneumoniae isolates, particularly the role of the ST661 that, despite being a rare lineage, harbors the blaVIM gene and is associated with high biofilm production and the highest mortality rates.
Meropenem/vaborbactam activity against carbapenem-resistant Klebsiella pneumoniae from catheter-related bloodstream infections Francesca Sivori, Massimo Francalancia, Mauro Truglio, Ilaria Cavallo, Carmelina Pronesti, Giorgia Fabrizio, Ilaria Celesti, Andrea Cazzani, Lorenzo Furzi, Fulvia Pimpinelli, Enea Gino Di Domenico Frontiers in Cellular and Infection Microbiology, 2025 IntroductionCarbapenem-resistant Klebsiella pneumoniae (CRKP) poses a significant threat in oncology settings due to its multidrug resistance and ability to form biofilms on indwelling medical devices.MethodsThis study investigated the in vitro and in vivo activity of meropenem/vaborbactam (MEV) against two CRKP isolates recovered from catheter-related bloodstream infections in patients undergoing orthopedic oncologic surgery.ResultsWhole-genome sequencing identified the isolates as ST101 and ST307, harboring resistance determinants including blaKPC-3 and blaOXA-1, distributed across IncFII and IncFIB plasmid replicons. Both isolates exhibited extensive resistance to β-lactams, aminoglycosides, and fluoroquinolones but remained susceptible to MEV. Phenotypic assays revealed enhanced biofilm formation and metabolic activity compared to the reference strain Kp ATCC 13883 in the absence of hypervirulence-associated genes. MEV demonstrated bactericidal activity against both planktonic and biofilm-associated cells, with minimum bactericidal concentration (MBC90) and minimum biofilm eradication concentration (MBEC90) values of 0.5/8 μg/ml for CRKP ST101, 0.12/8 μg/ml for CRKP ST307, and 0.25/8 μg/ml for the Kp ATCC 13883 strain. In the Galleria mellonella infection model, MEV significantly improved larval survival following the CRKP challenge.DiscussionThese findings demonstrate that MEV exhibits activity against planktonic and biofilm-associated CRKP cells and highlight the need for further investigation in managing catheter-related bloodstream infections caused by multidrug-resistant K. pneumoniae.
Genomic characterization and antibiotic susceptibility of biofilm-forming Borrelia afzelii and Borrelia garinii from patients with erythema migrans Giorgia Fabrizio, Ilaria Cavallo, Francesca Sivori, Mauro Truglio, Daniela Kovacs, Massimo Francalancia, Giovanna D’Agosto, Elisabetta Trento, Grazia Prignano, Arianna Mastrofrancesco, Eva Ruzič-Sabljič, Fulvia Pimpinelli, Enea Gino Di Domenico Frontiers in Cellular and Infection Microbiology, 2025 BackgroundBorrelia afzelii and Borrelia garinii are the leading causes of Lyme borreliosis (LB) in Europe. Persistent LB forms may involve biofilms, potentially contributing to antibiotic tolerance.MethodsWhole genome sequencing (WGS) was conducted on 7 B. afzelii and 5 B. garinii isolates from erythema migrans skin biopsies. Biofilms were analyzed for extracellular DNA (eDNA) content and biomass. A phenol red metabolic assay assessed the minimum inhibitory concentration (MIC) and minimum biofilm inhibitory concentration (MBIC) of amoxicillin, azithromycin, ceftriaxone, and doxycycline.ResultsPhylogenetic analysis revealed B. afzelii and B. garinii formed distinct clades, while B. burgdorferi B31 clustered separately. Core genome analysis showed 38.9% of genes were shared between B. afzelii and B. garinii, decreasing to 26.1% with B. burgdorferi. The cloud genome expanded from 34.4% to 53.4% with the addition of B. burgdorferi. No antimicrobial resistance genes were detected. Surface adhesion gene profiles exhibited significant variation across species, suggesting potential functional differences in host adaptation. B. afzelii and B. garinii species exhibited biofilms, with biomass correlating significantly with eDNA production. MIC values were 0.25 μg/mL (amoxicillin, ceftriaxone), 0.125 μg/mL (azithromycin), and 0.5 μg/mL (doxycycline), with no significant interspecies differences. However, MBIC values were considerably higher: 2 μg/mL (amoxicillin, azithromycin), 16 μg/mL (ceftriaxone), and 32 μg/mL (doxycycline).ConclusionsBiofilms in B. afzelii and B. garinii significantly reduce antibiotic efficacy, particularly ceftriaxone and doxycycline. These in vitro findings highlight the need for targeted therapeutic strategies and suggest biofilms may impact treatment outcomes in LB.
Modulating the skin mycobiome-bacteriome and treating seborrheic dermatitis with a probiotic-enriched oily suspension Mauro Truglio, Francesca Sivori, Ilaria Cavallo, Elva Abril, Valerio Licursi, Giorgia Fabrizio, Giorgia Cardinali, Marco Pignatti, Luigi Toma, Floriana Valensise, Antonio Cristaudo, Fulvia Pimpinelli, Enea Gino Di Domenico Scientific Reports, 2024 Seborrheic dermatitis (SD) affects 2–5% of the global population, with imbalances in the skin microbiome implicated in its development. This study assessed the impact of an oily suspension containing Lactobacillus crispatus P17631 and Lacticaseibacillus paracasei I1688 (termed EUTOPLAC) on SD symptoms and the skin mycobiome-bacteriome modulation. 25 SD patients were treated with EUTOPLAC for a week. Symptom severity and skin mycobiome-bacteriome changes were measured at the start of the treatment (T0), after seven days (T8), and three weeks post-treatment (T28). Results indicated symptom improvement post-EUTOPLAC, with notable reductions in the Malassezia genus. Concurrently, bacterial shifts were observed, including a decrease in Staphylococcus and an increase in Lactobacillus and Lacticaseibacillus. Network analysis highlighted post-EUTOPLAC instability in fungal and bacterial interactions, with increased negative correlations between Malassezia and Lactobacillus and Lacticaseibacillus genera. The study suggests EUTOPLAC's potential as a targeted SD treatment, reducing symptoms and modulating the mycobiome-bacteriome composition.
Biofilm-mediated antibiotic tolerance in Staphylococcus aureus from spinal cord stimulation device-related infections Francesca Sivori, Ilaria Cavallo, Mauro Truglio, Lorella Pelagalli, Valerio Mariani, Giorgia Fabrizio, Elva Abril, Iolanda Santino, Piera Assunta Fradiani, Mariacarmela Solmone, Fulvia Pimpinelli, Luigi Toma, Roberto Arcioni, Roberto Alberto De Blasi, Enea Gino Di Domenico Microbiology Spectrum, 2024 Staphylococcus aureus is a predominant cause of infections in individuals with spinal cord stimulation (SCS) devices. Biofilm formation complicates these infections, commonly requiring both surgical and antibiotic treatments. This study explored the biofilm matrix composition and antimicrobial susceptibility of planktonic and biofilm-growing S. aureus isolates from individuals with SCS-related infections. Whole-genome sequencing (WGS) examined genotypes, virulome, resistome, and the pan-genome structure. The study also analyzed biofilm matrix composition, early surface adhesion, hemolytic activity, and antibiotic-susceptibility testing. WGS revealed genetic diversity among isolates. One isolate, though oxacillin susceptible, contained the mec A gene. The median number of virulence factor genes per isolate was 58. All isolates harbored the biofilm-related ica A/D genes. When assessing phenotypic characteristics, all strains demonstrated the ability to form biofilms in vitro . The antimicrobial susceptibility profile indicated that oxacillin, rifampin, and teicoplanin showed the highest efficacy against S. aureus biofilm. Conversely, high biofilm tolerance was observed for vancomycin, trimethoprim/sulfamethoxazole, and levofloxacin. These findings suggest that S. aureus isolates are highly virulent and produce robust biofilms. In cases of suspected biofilm infections caused by S. aureus , vancomycin should not be the primary choice due to its low activity against biofilm. Instead, oxacillin, rifampin, and teicoplanin appear to be more effective options to manage SCS infections. IMPORTANCE SCS devices are increasingly used to manage chronic pain, but infections associated with these devices, particularly those caused by Staphylococcus aureus , present significant clinical challenges. These infections are often complicated by biofilm formation, which protects bacteria from immune responses and antibiotic treatments, making them difficult to eradicate. Understanding the genetic diversity, virulence, and biofilm characteristics of S. aureus isolates from SCS infections is critical to improving treatment strategies. Our study highlights the need to reconsider commonly used antibiotics like vancomycin, which shows reduced activity against biofilm-growing cells. Identifying more effective alternatives, such as oxacillin, rifampin, and teicoplanin, provides valuable insight for clinicians when managing biofilm-related S. aureus infections in patients with SCS implants. This research contributes to the growing evidence that biofilm formation is crucial in treating device-related infections, emphasizing the importance of tailoring antimicrobial strategies to the biofilm phenotype.
Staphylococcus aureus colonizing the skin microbiota of adults with severe atopic dermatitis exhibits genomic diversity and convergence in biofilm traits Francesca Sivori, Ilaria Cavallo, Mauro Truglio, Flavio De Maio, Maurizio Sanguinetti, Giorgia Fabrizio, Valerio Licursi, Massimo Francalancia, Fulvia Fraticelli, Ilenia La Greca, Federica Lucantoni, Emanuela Camera, Maria Mariano, Fiorentina Ascenzioni, Antonio Cristaudo, Fulvia Pimpinelli, Enea Gino Di Domenico Biofilm, 2024 Atopic dermatitis (AD) is a chronic inflammatory skin disorder exacerbated by Staphylococcus aureus colonization. The specific factors that drive S. aureus overgrowth and persistence in AD remain poorly understood. This study analyzed skin barrier functions and microbiome diversity in lesional (LE) and non-lesional (NL) forearm sites of individuals with severe AD compared to healthy control subjects (HS). Notable differences were found in transepidermal water loss, stratum corneum hydration, and microbiome composition. Cutibacterium was more prevalent in HS, while S. aureus and S. lugdunensis were predominantly found in AD LE skin. The results highlighted that microbial balance depends on inter-species competition. Specifically, network analysis at the genus level demonstrated that overall bacterial correlations were higher in HS, indicating a more stable microbial community. Notably, network analysis at the species level revealed that S. aureus engaged in competitive interactions in NL and LE but not in HS. Whole-genome sequencing (WGS) showed considerable genetic diversity among S. aureus strains from AD. Despite this variability, the isolates exhibited convergence in key phenotypic traits such as adhesion and biofilm formation, which are crucial for microbial persistence. These common phenotypes suggest an adaptive evolution, driven by competition in the AD skin microenvironment, of S. aureus and underscoring the interplay between genetic diversity and phenotypic convergence in microbial adaptation. • Cutibacterium is prevalent on healthy skin; S. aureus dominates AD lesions. • S. aureus engages in competitive interactions in AD microenvironments. • S. aureus in AD shows genetic diversity with phenotypic similarity. • Biofilm and adhesion traits ensure persistence in AD skin.
Skin manifestations and human immunodeficiency virus infection in the Tigray region, Ethiopia: Implications for clinical management and epidemiologic surveillance Aldo Morrone, Elva Abril, Ilaria Cavallo, Francesca Sivori, Isabella Sperduti, Viviana Lora, Giovanna D'Agosto, Elisabetta Trento, Martina Pontone, Arianna Mastrofrancesco, Abraham Getachew Kelbore, Frehiwot Daba Gutema, Adel Sammain, Ottavio Latini, Enea Gino Di Domenico, Fulvia Pimpinelli JEADV Clinical Practice, 2024 BackgroundPatients with human immunodeficiency virus (HIV) infection may present a large variety of skin manifestations, often associated with significant morbidity. In turn, dermatological diseases may represent an early sign of HIV infection, particularly in resource‐limited settings.ObjectivesThis study aimed to assess the spectrum of dermatological diseases and their potential value as clinical proxies for the early detection and management of HIV in a rural region of Ethiopia.MethodsThe study was performed on a population of 67,161 patients with skin diseases attending the Italian Dermatological Center in Mekele, Tigray region, Ethiopia. HIV infection was diagnosed in 1892 individuals (1065 female), all naïve to antiretroviral therapy.ResultsInfectious skin diseases were present in 57.2% of the total HIV population. Among the infectious skin manifestations, dermatophytosis (20.5%), impetigo (5.9%), candidiasis (4.7%) and molluscum contagiosum (4.7%) were significantly more represented in patients with HIV infection (p < 0.001). Regarding the noninfectious manifestations, pruritus and atrophy of the papillae on the tongue were significantly associated with HIV (p < 0.001). Notably, females had a significantly higher incidence of dermatophytosis and seborrheic dermatitis as compared to their male counterparts (p < 0.001), whereas scabies, psoriasis and leishmaniasis were significantly more frequent in males (p < 0.001).ConclusionsSkin manifestations are common in HIV patients, often reflecting compromised immune status. In addition, Dermatophytosis and pruritus were the most frequently reported manifestations of HIV, thus representing useful clinical proxies to raise the suspicion of an underlying HIV infection. Besides, gender differences in skin manifestations should also be considered in the clinical evaluation.
Bacterial Biofilm in Chronic Wounds and Possible Therapeutic Approaches Ilaria Cavallo, Francesca Sivori, Arianna Mastrofrancesco, Elva Abril, Martina Pontone, Enea Gino Di Domenico, Fulvia Pimpinelli Biology, 2024 Wound repair and skin regeneration is a very complex orchestrated process that is generally composed of four phases: hemostasis, inflammation, proliferation, and remodeling. Each phase involves the activation of different cells and the production of various cytokines, chemokines, and other inflammatory mediators affecting the immune response. The microbial skin composition plays an important role in wound healing. Indeed, skin commensals are essential in the maintenance of the epidermal barrier function, regulation of the host immune response, and protection from invading pathogenic microorganisms. Chronic wounds are common and are considered a major public health problem due to their difficult-to-treat features and their frequent association with challenging chronic infections. These infections can be very tough to manage due to the ability of some bacteria to produce multicellular structures encapsulated into a matrix called biofilms. The bacterial species contained in the biofilm are often different, as is their capability to influence the healing of chronic wounds. Biofilms are, in fact, often tolerant and resistant to antibiotics and antiseptics, leading to the failure of treatment. For these reasons, biofilms impede appropriate treatment and, consequently, prolong the wound healing period. Hence, there is an urgent necessity to deepen the knowledge of the pathophysiology of delayed wound healing and to develop more effective therapeutic approaches able to restore tissue damage. This work covers the wound-healing process and the pathogenesis of chronic wounds infected by biofilm-forming pathogens. An overview of the strategies to counteract biofilm formation or to destroy existing biofilms is also provided.
Microbial biofilm correlates with an increased antibiotic tolerance and poor therapeutic outcome in infective endocarditis Enea Gino Di Domenico, Sara Giordana Rimoldi, Ilaria Cavallo, Giovanna D’Agosto, Elisabetta Trento, Giovanni Cagnoni, Alessandro Palazzin, Cristina Pagani, Francesca Romeri, Elena De Vecchi, Monica Schiavini, Daniela Secchi, Carlo Antona, Giuliano Rizzardini, Rita Barbara Dichirico, Luigi Toma, Daniela Kovacs, Giorgia Cardinali, Maria Teresa Gallo, Maria Rita Gismondo, Fabrizio Ensoli BMC Microbiology, 2019
The emerging role of microbial biofilm in lyme neuroborreliosis Enea Gino Di Domenico, Ilaria Cavallo, Valentina Bordignon, Giovanna D'Agosto, Martina Pontone, Elisabetta Trento, Maria Teresa Gallo, Grazia Prignano, Fulvia Pimpinelli, Luigi Toma, Fabrizio Ensoli Frontiers in Neurology, 2018
