2023 - Università degli Studi di Milano - Specialist-Board Certified in Infectious and Tropical Diseases
2018 - Università degli Studi di Milano - Doctor of Medicine
Integrating artificial intelligence with genome sequencing against antimicrobial resistance: a narrative review Giovanni Scaglione, Nicolò Mastroianni, Alberto Rizzo, Emanuele Palomba, Davide Carcione, et al. Frontiers in Public Health, 2026 Antimicrobial resistance (AMR) represents an escalating global health threat, demanding diagnostic strategies capable of rapid, accurate, and comprehensive pathogen characterization. Genomic sequencing has transformed our ability to elucidate resistance mechanisms and track their evolution, yet its routine clinical adoption remains limited by cost, workflow constraints, and extended turnaround times. This narrative review examines how artificial intelligence (AI) and machine learning (ML) can enhance and operationalize sequencing-based diagnostics across the clinical microbiology continuum. We summarize current AI applications in whole-genome sequencing for AMR prediction, pan-genome feature extraction, and multicenter model generalizability, including emerging approaches such as federated learning. We then explore AI-driven metagenomic analytics for pathogen detection, resistome profiling, outbreak investigation, and prognostic modeling. Complementary non-genomic technologies, Raman spectroscopy and MALDI-TOF MS, are also evaluated for their potential to deliver rapid resistance profiling when integrated with ML. Finally, we discuss practical barriers, including cost, dataset standardization, interpretability, and regulatory challenges, while outlining future directions toward scalable, explainable, and equitable AI-guided diagnostics. Integrating AI with genomic and rapid phenotypic tools offers a pathway to real-time surveillance, optimized antimicrobial stewardship, and strengthened preparedness against emerging infectious threats.
Microbial signatures and host immune responses associated with the development of ventilator-associated pneumonia among patients with neurological injuries Leonardo Mancabelli, Emanuele Palomba, Federico Magni, Liliane Chatenoud, Ilaria Olgiati, et al. Microbiology Spectrum, 2026 Ventilator-associated pneumonia (VAP) remains a leading complication in mechanically ventilated patients, yet the contribution of the respiratory microbiota remains poorly understood. The PULMIVAP study is a multicenter, longitudinal cohort investigation of respiratory microbiota composition and host immune responses in critically ill adults intubated for non-pulmonary conditions. A total of 146 intubated adult patients were enrolled across eight Italian ICUs, forming matched groups of 73 with VAP and 73 without. Oropharyngeal swabs and endotracheal aspirates were collected at intubation and either at VAP diagnosis or at a matched point in controls for a total of 584 biological samples. Metataxonomic analyses revealed substantial temporal shifts in microbial communities across both upper and lower respiratory compartments, with a trend toward reduced microbial richness in patients who developed VAP. Several genera, such as Corynebacterium, were more abundant in no-VAP patients, whereas Escherichia-Shigella and Peptoniphilus were enriched in VAP samples. Cytokine-microbiota correlation analysis suggested a pro-inflammatory signature in VAP patients, with Citrobacter positively associated with IFN-γ and TNF-α, while several commensal genera were inversely correlated with inflammatory mediators. Additionally, taxa associated with VAP correlated with lower PaO 2 /FiO 2 ratios, implicating them in disease severity. Consistently, several bacteria, such as Corynebacterium , appeared to be linked to better respiratory outcomes, suggesting protective or risk-associated microbial profiles. Overall, these findings highlight the complex interplay between microbial communities and mucosal immunity in the pathogenesis of VAP. The identification of condition-associated microbial and immunological signatures may inform future strategies for risk stratification and targeted prevention. IMPORTANCE Ventilator-associated pneumonia (VAP) remains a major complication of mechanical ventilation, yet most microbiome studies have focused on late-stage infection or single airway compartments, limiting insight into early microbial dynamics associated with VAP risk. By longitudinally characterizing upper and lower airway microbiota before and during VAP development, this study provides new insights into microbial and immune patterns associated with susceptibility and disease severity in humans. These findings contribute to the current understanding of VAP pathogenesis by suggesting a role for early airway dysbiosis and local immune responses alongside clinical factors. Remarkably, the identification of taxa associated with risk or protection supports the potential for microbiota-informed monitoring and future risk stratification strategies during mechanical ventilation. CLINICAL TRIALS This study is registered with ClinicalTrials.gov as NCT04849039 .
Hospital Acquired Infections Among Solid Organ Transplant Recipients Hospitalized in Intensive Care Unit (2018–2024): A Study of the GiViTI Group Camilla Genovese, Martina Offer, Marta Colaneri, Francesca Dore, Giorgia Montrucchio, et al. Transplant Infectious Disease, 2025 Introduction Limited data exist regarding the burden of intensive care unit (ICU)‐acquired infections in the early post‐solid organ transplant (SOT) period, particularly in multidrug resistant organisms‐endemic settings. This study aims at describing the epidemiology, clinical characteristics, and outcomes of patients who developed an ICU‐acquired infection following a SOT procedure in Italy from 2018 to 2024. Methods A multicenter, retrospective study was conducted within the Italian PROSAFE project across 31 ICUs from 2018 to 2024. All adult patients admitted to ICU during the same hospitalization as their organ transplant procedure were included. Bloodstream infections, ventilator associated pneumonia, intra‐abdominal infections, and urinary tract infections occurring more than 48 h after ICU admission were retrieved. Results Among 2210 SOT recipients, 154 (6.9%) developed 193 ICU‐acquired infections. Ventilator associated pneumonia was the most frequent (74, 38.3%), followed by bloodstream infections (56, 29%). Multidrug resistant organisms were identified in 34/87 (39%) isolates with available antibiogram. ICU‐acquired infections were associated with significantly higher intra‐ICU mortality (35/154, 22.4% vs. 49/2056, 2.4%; p < 0.001) and longer ICU stays (24 vs. 4 days; p < 0.001). Patients with infections due to multidrug resistant organisms showed higher mortality and length of stay. Conclusions ICU‐acquired infections occurred in nearly 7% of SOT recipients admitted to ICU following a SOT procedure, with a significant contribute of multidrug resistant organisms. These infections were associated with striking differences in mortality and length of stay. Finally, this study suggested that patients with MDRO infections showed trends toward higher mortality and length of stay.
Effectiveness of Vascular Catheter Removal Versus Retention in Non-ICU Patients with CRBSI or CABSI in Retrospective, Single-Center Study Giovanni De Capitani, Marta Colaneri, Claudia Conflitti, Fabio Borgonovo, Lucia Galli, et al. Microorganisms, 2025 Catheter-associated bloodstream infections (CABSIs) and catheter-related bloodstream infections (CRBSIs) are significant causes of morbidity and mortality worldwide. The current practice favors the removal of vascular access devices (VADs); however, the evidence on this topic remains inconclusive. This study evaluates the clinical outcomes in terms of in-hospital mortality and catheter retention vs. removal in CABSI and CRBSI cases. A retrospective, observational, single-center study was conducted at Luigi Sacco Hospital, Milan, Italy (May 2021–December 2023), and it analyzed non-ICU adult patients with VADs diagnosed with CRBSIs or CABSIs. Clinical and microbiological data were collected to assess the outcomes based on catheter management. Among 1874 patients with VADs, 147 were included, with 164 VAD infection events (92 CABSIs and 72 CRBSIs). Overall, 35 (23.8%) patients with CABSIs and CRBSIs died. Out of those who retained the catheter 19 (35.8%) patients died, while among removal patients 16 (17%) died (p = 0.018). A Candida spp. isolation was found to be significantly associated with a higher likelihood of catheter removal (p = 0.04). Our findings suggest that, in non-ICU CRBSI and CABSI cases, VAD removal may be associated with improved outcomes when feasible.
Antiviral Treatments for Influenza Emanuele Palomba, Valeria Castelli, Giulia Renisi, Alessandra Bandera, Andrea Lombardi, et al. Seminars in Respiratory and Critical Care Medicine, 2021
Ventilator-Associated Pneumonia Due to ESBL-Producing Escherichia coli Successfully Treated with Cefepime/Enmetazobactam: A European Case Report B Viaggi, T Giani, E Palomba, A Gori, A Farese, GM Rossolini, M Colaneri Infectious Diseases and Therapy, 1-8 , 2026 2026
Microbial signatures and host immune responses associated with the development of ventilator-associated pneumonia among patients with neurological injuries L Mancabelli, E Palomba, F Magni, L Chatenoud, I Olgiati, C Buracchi, ... Microbiology spectrum 14 (5), e03193-25 , 2026 2026
Correction: Integrating artificial intelligence with genome sequencing against antimicrobial resistance: a narrative review G Scaglione, N Mastroianni, A Rizzo, E Palomba, D Carcione, SG Rimoldi, ... Frontiers in Public Health 14, 1824508 , 2026 2026
Epidemiology, resistance patterns, and outcomes of candidemia acquired in Italian intensive care units: insights from the GIVITI network (2020–2024) G Scaglione, M Colaneri, M Offer, G Montrucchio, C Genovese, B Viaggi, ... Critical Care , 2026 2026
Gastritis and AIDS-related cholangiopathy as an unusual presentation of HIV infection F Brivio, A Covizzi, D Bernasconi, G Gubertini, M Schiavini, S Grosso, ... Gastroenterology Report 14, goag017 , 2026 2026
Integrating artificial intelligence with genome sequencing against antimicrobial resistance: a narrative review G Scaglione, N Mastroianni, A Rizzo, E Palomba, D Carcione, G Brigante, ... Frontiers in Public Health 14, 1757161 , 2026 2026 Citations: 3
Integrating artificial intelligence G Scaglione, N Mastroianni, A Rizzo, E Palomba, D Carcione, G Brigante, ... 2026
Hospital Acquired Infections Among Solid Organ Transplant Recipients Hospitalized in Intensive Care Unit (2018–2024): A Study of the GiViTI Group C Genovese, M Offer, M Colaneri, F Dore, G Montrucchio, G Scaglione, ... Transplant Infectious Disease 27 (6), e70120 , 2025 2025 Citations: 3
Exploring human use of monoclonal antibodies against critical bacteria: a scoping review of clinical trials M Piscaglia, G Scaglione, C Genovese, F Borgonovo, F Brivio, ... Infectious Diseases and Therapy 14 (8), 1619-1647 , 2025 2025 Citations: 10
Incidence, microbiology, and mortality of ventilation-associated pneumonia in a large Italian cohort of critically ill patients: results from the PROSAFE project M Colaneri, G Montrucchio, G Scaglione, G Monti, G Tricella, C Genovese, ... Clinical Microbiology and Infection , 2025 2025 Citations: 13
Effectiveness of vascular catheter removal versus retention in Non-ICU patients with CRBSI or CABSI in Retrospective, Single-Center study G De Capitani, M Colaneri, C Conflitti, F Borgonovo, L Galli, G Scaglione, ... Microorganisms 13 (5), 1085 , 2025 2025 Citations: 1
Activity of imipenem/relebactam against KPC-producing Klebsiella pneumoniae and the possible role of Ompk36 mutation in determining resistance: an Italian retrospective analysis E Palomba, A Comelli, F Saluzzo, F Di Marco, E Matarazzo, NL Re, ... Annals of Clinical Microbiology and Antimicrobials 24 (1), 23 , 2025 2025 Citations: 8
P01. The IMPACT-VAP study: incidence and mortality of ventilator-associated pneumonia in critically ill patients: results from the PROSAFE project M Colaneri, G Montrucchio, G Scaglione, M Offer, G Tricella, C Genovese, ... JAC-Antimicrobial Resistance 7 (Supplement_2), dlaf046. 001 , 2025 2025
Understanding the burden of antibiotic resistance: a decade of carbapenem-resistant Gram-negative bacterial infections in Italian intensive care units (vol 15, 1405390, 2024) G Scaglione, M Perego, M Colaneri, C Genovese, F Brivio, A Covizzi, ... FRONTIERS IN MICROBIOLOGY 16 , 2025 2025
Corrigendum: Understanding the burden of antibiotic resistance: a decade of carbapenem-resistant Gram-negative bacterial infections in Italian intensive care units G Scaglione, M Perego, M Colaneri, C Genovese, F Brivio, A Covizzi, ... Frontiers in Microbiology 16, 1584655 , 2025 2025 Citations: 2
P-229. Epidemiology of catheter-related bloodstream infections in italian intensive care units: data from the Italian network for the evaluation of ICU interventions C Genovese, M Perego, G Scaglione, E Palomba, G Giordano, V Breschi, ... Open Forum Infectious Diseases 12 (Suppl 1), ofae631. 433 , 2025 2025 Citations: 1
Solid organ transplant in recipients with ongoing SARS-CoV-2 infection: a systematic review of case reports and series A Lombardi, M Colaneri, C Azzarà, P Saltini, G Viero, E Palomba, ... International Journal of Infectious Diseases 147, 107214 , 2024 2024 Citations: 6
Understanding the burden of antibiotic resistance: a decade of carbapenem-resistant Gram-negative bacterial infections in Italian intensive care units G Scaglione, M Perego, M Colaneri, C Genovese, F Brivio, A Covizzi, ... Frontiers in microbiology 15, 1405390 , 2024 2024 Citations: 11
Epidemiology, clinical manifestations, and outcome of mucormycosis in solid organ transplant recipients: a systematic review of reported cases E Palomba, M Colaneri, C Azzarà, M Fava, A Maccaro, G Renisi, G Viero, ... Open Forum Infectious Diseases 11 (6), ofae043 , 2024 2024 Citations: 13
Clinical characteristics and outcomes of vaccinated patients hospitalised with SARS-CoV-2 breakthrough infection: Multi-IPV, a multicentre study in Northern Italy A Lombardi, S Villa, M Colaneri, G Scaglione, F Bai, B Varisco, V Bono, ... Journal of Infection and Public Health 17 (3), 467-473 , 2024 2024 Citations: 3
MOST CITED SCHOLAR PUBLICATIONS
Characteristics of 1573 healthcare workers who underwent nasopharyngeal swab testing for SARS-CoV-2 in Milan, Lombardy, Italy A Lombardi, D Consonni, M Carugno, G Bozzi, D Mangioni, A Muscatello, ... Clinical microbiology and infection 26 (10), 1413. e9-1413. e13 , 2020 2020 Citations: 157
Gut and airway microbiota dysbiosis and their role in COVID-19 and long-COVID G Ancona, L Alagna, C Alteri, E Palomba, A Tonizzo, A Pastena, ... Frontiers in immunology 14, 1080043 , 2023 2023 Citations: 125
Anakinra combined with methylprednisolone in patients with severe COVID-19 pneumonia and hyperinflammation: An observational cohort study G Bozzi, D Mangioni, F Minoia, S Aliberti, G Grasselli, L Barbetta, ... Journal of Allergy and Clinical Immunology 147 (2), 561-566. e4 , 2021 2021 Citations: 122
Early phases of COVID-19 are characterized by a reduction in lymphocyte populations and the presence of atypical monocytes A Lombardi, E Trombetta, A Cattaneo, V Castelli, E Palomba, M Tirone, ... Frontiers in immunology 11, 560330 , 2020 2020 Citations: 80
Immune checkpoint inhibitors in people living with HIV/AIDS: facts and controversies V Castelli, A Lombardi, E Palomba, G Bozzi, R Ungaro, L Alagna, ... Cells 10 (9), 2227 , 2021 2021 Citations: 37
Multidrug-resistant gram-negative bacteria decolonization in immunocompromised patients: a focus on fecal microbiota transplantation L Alagna, E Palomba, D Mangioni, G Bozzi, A Lombardi, R Ungaro, ... International Journal of Molecular Sciences 21 (16), 5619 , 2020 2020 Citations: 35
Treatment of SARS-CoV-2 relapse with remdesivir and neutralizing antibodies cocktail in a patient with X-linked agammaglobulinaemia E Palomba, M Carrabba, G Zuglian, L Alagna, P Saltini, V Fortina, C Hu, ... International Journal of Infectious Diseases 110, 338-340 , 2021 2021 Citations: 31
Nocardia infections in the immunocompromised host: a case series and literature review E Palomba, A Liparoti, A Tonizzo, V Castelli, L Alagna, G Bozzi, R Ungaro, ... Microorganisms 10 (6), 1120 , 2022 2022 Citations: 27
The interplay between gut microbiota and the immune system in liver transplant recipients and its role in infections G Ancona, L Alagna, A Lombardi, E Palomba, V Castelli, G Renisi, ... Infection and Immunity 89 (11) , 2021 2021 Citations: 26
Antiviral treatments for influenza E Palomba, V Castelli, G Renisi, A Bandera, A Lombardi, A Gori Seminars in Respiratory and Critical Care Medicine 42 (06), 859-872 , 2021 2021 Citations: 21
Multidrug-resistant bacterial colonization and infections in large retrospective cohort of mechanically ventilated COVID-19 patients D Mangioni, L Chatenoud, J Colombo, E Palomba, FA Guerrero, M Bolis, ... Emerging infectious diseases 29 (8), 1598 , 2023 2023 Citations: 15
Comparison of multiple definitions for ventilator-associated pneumonia in patients requiring mechanical ventilation for non-pulmonary conditions: preliminary data from PULMIVAP … L Alagna, E Palomba, L Chatenoud, R Massafra, F Magni, L Mancabelli, ... Journal of Hospital Infection 140, 90-95 , 2023 2023 Citations: 14
Incidence, microbiology, and mortality of ventilation-associated pneumonia in a large Italian cohort of critically ill patients: results from the PROSAFE project M Colaneri, G Montrucchio, G Scaglione, G Monti, G Tricella, C Genovese, ... Clinical Microbiology and Infection , 2025 2025 Citations: 13
Epidemiology, clinical manifestations, and outcome of mucormycosis in solid organ transplant recipients: a systematic review of reported cases E Palomba, M Colaneri, C Azzarà, M Fava, A Maccaro, G Renisi, G Viero, ... Open Forum Infectious Diseases 11 (6), ofae043 , 2024 2024 Citations: 13
Understanding the burden of antibiotic resistance: a decade of carbapenem-resistant Gram-negative bacterial infections in Italian intensive care units G Scaglione, M Perego, M Colaneri, C Genovese, F Brivio, A Covizzi, ... Frontiers in microbiology 15, 1405390 , 2024 2024 Citations: 11
Exploring human use of monoclonal antibodies against critical bacteria: a scoping review of clinical trials M Piscaglia, G Scaglione, C Genovese, F Borgonovo, F Brivio, ... Infectious Diseases and Therapy 14 (8), 1619-1647 , 2025 2025 Citations: 10
New antibiotics against multidrug-resistant Gram-negative bacteria in liver transplantation: clinical perspectives, toxicity, and PK/PD properties A Lombardi, L Alagna, E Palomba, G Viero, A Tonizzo, D Mangioni, ... Transplant International 37, 11692 , 2024 2024 Citations: 10
Incidence, microbiological and immunological characteristics of ventilator-associated pneumonia assessed by bronchoalveolar lavage and endotracheal aspirate in a prospective … D Mangioni, M Panigada, E Palomba, C Bobbio, L Chatenoud, L Alagna, ... Critical Care 27 (1), 369 , 2023 2023 Citations: 10
Activity of imipenem/relebactam against KPC-producing Klebsiella pneumoniae and the possible role of Ompk36 mutation in determining resistance: an Italian retrospective analysis E Palomba, A Comelli, F Saluzzo, F Di Marco, E Matarazzo, NL Re, ... Annals of Clinical Microbiology and Antimicrobials 24 (1), 23 , 2025 2025 Citations: 8
Exploring post-SEPSIS and post-COVID-19 syndromes: crossovers from pathophysiology to therapeutic approach D Holmes, M Colaneri, E Palomba, A Gori Frontiers in Medicine 10, 1280951 , 2024 2024 Citations: 8