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Article ; Online: Optimising machine learning prediction of minimum inhibitory concentrations in

Batisti Biffignandi, Gherard / Chindelevitch, Leonid / Corbella, Marta / Feil, Edward J / Sassera, Davide / Lees, John A

Microbial genomics

2024 Volume 10, Issue 3

Abstract: Minimum Inhibitory Concentrations (MICs) are the gold standard for quantitatively measuring antibiotic resistance. However, lab-based MIC determination can be time-consuming and suffers from low reproducibility, and interpretation as sensitive or ... ...

Abstract	Minimum Inhibitory Concentrations (MICs) are the gold standard for quantitatively measuring antibiotic resistance. However, lab-based MIC determination can be time-consuming and suffers from low reproducibility, and interpretation as sensitive or resistant relies on guidelines which change over time. Genome sequencing and machine learning promise to allow
MeSH term(s)	Klebsiella pneumoniae/genetics ; Reproducibility of Results ; Anti-Bacterial Agents/pharmacology ; Machine Learning ; Microbial Sensitivity Tests
Chemical Substances	Anti-Bacterial Agents
Language	English
Publishing date	2024-03-26
Publishing country	England
Document type	Journal Article
ZDB-ID	2835258-0
ISSN	2057-5858 ; 2057-5858
ISSN (online)	2057-5858
ISSN	2057-5858
DOI	10.1099/mgen.0.001222
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Article: Phenotypic and Genotypic Assays to Evaluate Coagulase-Negative Staphylococci Biofilm Production in Bloodstream Infections.

Grassia, Giulia / Bagnarino, Jessica / Siciliano, Mariangela / Barbarini, Daniela / Corbella, Marta / Cambieri, Patrizia / Baldanti, Fausto / Monzillo, Vincenzina

Microorganisms

2024 Volume 12, Issue 1

Abstract: Coagulase-negative staphylococci (CoNS) are commensal on human body surfaces and, for years, they were not considered a cause of bloodstream infection and were often regarded as contamination. However, the involvement of CoNS in nosocomial infection is ... ...

Abstract	Coagulase-negative staphylococci (CoNS) are commensal on human body surfaces and, for years, they were not considered a cause of bloodstream infection and were often regarded as contamination. However, the involvement of CoNS in nosocomial infection is increasingly being recognized. The insertion of cannulas and intravascular catheters represents the primary source of CoNS entry into the bloodstream, causing bacteremia and sepsis. They owe their pathogenic role to their ability to produce biofilms on surfaces, such as medical devices. In this study, we evaluate the adhesive capacity of CoNS isolated from blood cultures by comparing a spectrophotometric phenotypic assay with genotypic analysis based on the evidence of the
Language	English
Publishing date	2024-01-08
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2720891-6
ISSN	2076-2607
ISSN	2076-2607
DOI	10.3390/microorganisms12010126
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Article: Surveillance in a Neonatal Intensive Care Unit Allowed the Isolation of a Strain of VIM-Producing

Merla, Cristina / Mileto, Irene / Gaiarsa, Stefano / Achille, Cristian / Ghirardello, Stefano / Corbella, Marta / Baldanti, Fausto / Cambieri, Patrizia

Antibiotics (Basel, Switzerland)

2023 Volume 12, Issue 1

Abstract: Here, we describe the isolation of a strain of the ... ...

Abstract	Here, we describe the isolation of a strain of the genus
Language	English
Publishing date	2023-01-06
Publishing country	Switzerland
Document type	Case Reports
ZDB-ID	2681345-2
ISSN	2079-6382
ISSN	2079-6382
DOI	10.3390/antibiotics12010098
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Article ; Online: The COVID-19 Pandemic Sparked Off a Large-Scale Outbreak of Carbapenem-Resistant Acinetobacter baumannii from the Endemic Strains at an Italian Hospital.

Petazzoni, Greta / Bellinzona, Greta / Merla, Cristina / Corbella, Marta / Monzillo, Vincenzina / Samuelsen, Ørjan / Corander, Jukka / Sassera, Davide / Gaiarsa, Stefano / Cambieri, Patrizia

Microbiology spectrum

2023 , Page(s) e0450522

Abstract: Acinetobacter baumannii is a nosocomial pathogen that poses a serious threat due to the rise of incidence of multidrug-resistant (MDR) strains. During the COVID-19 pandemic, MDR A. baumannii clones have caused several outbreaks worldwide. Here, we ... ...

Abstract	Acinetobacter baumannii is a nosocomial pathogen that poses a serious threat due to the rise of incidence of multidrug-resistant (MDR) strains. During the COVID-19 pandemic, MDR A. baumannii clones have caused several outbreaks worldwide. Here, we describe a detailed investigation of an MDR A. baumannii outbreak that occurred at Policlinico San Matteo (Pavia, Italy). A total of 96 A. baumannii strains, isolated between January and July 2020 from 41 inpatients (both SARS-CoV-2 positive and negative) in different wards, were characterized by phenotypic and genomic analyses combining Illumina and Nanopore sequencing. Antibiotic susceptibility testing revealed that all isolates were resistant to carbapenems, and the sequence analysis attributed this to the carbapenemase gene
Language	English
Publishing date	2023-03-23
Publishing country	United States
Document type	Journal Article
ZDB-ID	2807133-5
ISSN	2165-0497 ; 2165-0497
ISSN (online)	2165-0497
ISSN	2165-0497
DOI	10.1128/spectrum.04505-22
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Article ; Online: Clinical isolates of ST131

Piazza, Aurora / Corbella, Marta / Mattioni Marchetti, Vittoria / Merla, Cristina / Mileto, Irene / Kuka, Angela / Petazzoni, Greta / Gaiarsa, Stefano / Migliavacca, Roberta / Baldanti, Fausto / Cambieri, Patrizia

Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin

2024 Volume 29, Issue 8

Abstract: The dissemination of carbapenemase- ... ...

Abstract	The dissemination of carbapenemase-producing
MeSH term(s)	Humans ; Escherichia coli/genetics ; Escherichia coli Infections/diagnosis ; beta-Lactamases/genetics ; Carbapenem-Resistant Enterobacteriaceae ; Italy/epidemiology ; Europe ; Anti-Bacterial Agents/pharmacology ; Anti-Bacterial Agents/therapeutic use
Chemical Substances	beta-Lactamases (EC 3.5.2.6) ; Anti-Bacterial Agents
Language	English
Publishing date	2024-02-08
Publishing country	Sweden
Document type	Journal Article
ZDB-ID	1338803-4
ISSN	1560-7917 ; 1025-496X
ISSN (online)	1560-7917
ISSN	1025-496X
DOI	10.2807/1560-7917.ES.2024.29.8.2400073
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Article ; Online: Impact of Whole Genome Sequencing to investigate transmission of Serratia marcescens in Neonatal Intensive Care Unit.

Merla, Cristina / Ramus, Marina / Kuka, Angela / Mileto, Irene / Gaiarsa, Stefano / Di Comite, Amelia / Corbella, Marta / Piralla, Antonio / Lanave, Marina Liliana / Muzzi, Alba / Ghirardello, Stefano / Baldanti, Fausto / Cambieri, Patrizia

Journal of infection and public health

2024 Volume 17, Issue 5, Page(s) 918–921

Abstract: Newborns admitted to neonatal intensive care units (NICU) are at increased risk of health care-associated infections. Serratia marcescens represent the third most common pathogen in NICU outbreaks. Here we present an outbreak investigation performed ... ...

Abstract	Newborns admitted to neonatal intensive care units (NICU) are at increased risk of health care-associated infections. Serratia marcescens represent the third most common pathogen in NICU outbreaks. Here we present an outbreak investigation performed using Whole Genome Sequencing (WGS) analyses and the control measures implemented to limit the spread of S. marcescens in the NICU of an Italian hospital. In February 2023 S. marcescens was isolated from six newborns, when in 2022 this pathogen was isolated only from two samples in the same ward. Measures for infection prevention were adopted. Routinary surveillance screening, performed with rectal swabs collected at admission and weekly thereafter, was implemented to search for S. marcescens presence. Environmental samples were collected. All the isolates, obtained from the conjunctival swab of six newborns, from rectal swab of two newborns who did not develop infections, as well as from the aerators of two faucets, were sequenced. WGS analyses showed no correlation between the isolates from newborns and environmental isolates. The implementation of the measures for infection prevention and control had enabled us to successfully control the outbreak within a short period. WGS analyses proved to be crucial in outbreak investigation to limit the spreading of the pathogens.
MeSH term(s)	Humans ; Infant, Newborn ; Intensive Care Units, Neonatal ; Serratia marcescens/genetics ; Serratia Infections/diagnosis ; Cross Infection/prevention & control ; Disease Outbreaks/prevention & control ; Whole Genome Sequencing
Language	English
Publishing date	2024-03-28
Publishing country	England
Document type	Journal Article
ZDB-ID	2467587-8
ISSN	1876-035X ; 1876-0341
ISSN (online)	1876-035X
ISSN	1876-0341
DOI	10.1016/j.jiph.2024.03.025
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Article ; Online: Genetic barriers more than environmental associations explain Serratia marcescens population structure.

Sterzi, Lodovico / Nodari, Riccardo / Di Marco, Federico / Ferrando, Maria Laura / Saluzzo, Francesca / Spitaleri, Andrea / Allahverdi, Hamed / Papaleo, Stella / Panelli, Simona / Rimoldi, Sara Giordana / Batisti Biffignandi, Gherard / Corbella, Marta / Cavallero, Annalisa / Prati, Paola / Farina, Claudio / Cirillo, Daniela Maria / Zuccotti, Gianvincenzo / Bandi, Claudio / Comandatore, Francesco

Communications biology

2024 Volume 7, Issue 1, Page(s) 468

Abstract: Bacterial species often comprise well-separated lineages, likely emerged and maintained by genetic isolation and/or ecological divergence. How these two evolutionary actors interact in the shaping of bacterial population structure is currently not fully ... ...

Abstract	Bacterial species often comprise well-separated lineages, likely emerged and maintained by genetic isolation and/or ecological divergence. How these two evolutionary actors interact in the shaping of bacterial population structure is currently not fully understood. In this study, we investigate the genetic and ecological drivers underlying the evolution of Serratia marcescens, an opportunistic pathogen with high genomic flexibility and able to colonise diverse environments. Comparative genomic analyses reveal a population structure composed of five deeply-demarcated genetic clusters with open pan-genome but limited inter-cluster gene flow, partially explained by Restriction-Modification (R-M) systems incompatibility. Furthermore, a large-scale research on hundred-thousands metagenomic datasets reveals only a partial habitat separation of the clusters. Globally, two clusters only show a separate gene composition coherent with ecological adaptations. These results suggest that genetic isolation has preceded ecological adaptations in the shaping of the species diversity, an evolutionary scenario coherent with the Evolutionary Extended Synthesis.
MeSH term(s)	Serratia marcescens/genetics ; Genetic Variation ; Ecosystem ; Gene Flow ; Genomics
Language	English
Publishing date	2024-04-17
Publishing country	England
Document type	Journal Article
ISSN	2399-3642
ISSN (online)	2399-3642
DOI	10.1038/s42003-024-06069-w
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Article: Gut Microbiota and B Cell Receptor (BCR) Inhibitors for the Treatment of Chronic Lymphocytic Leukemia: Is Biodiversity Correlated with Clinical Response or Immune-Related Adverse Event Occurrence? A Cross-Sectional Study.

Zuccaro, Valentina / Petazzoni, Greta / Mileto, Irene / Corbella, Marta / Asperges, Erika / Sacchi, Paolo / Rattotti, Sara / Varettoni, Marzia / Defrancesco, Irene / Cambieri, Patrizia / Baldanti, Fausto / Arcaini, Luca / Bruno, Raffaele

Microorganisms

2023 Volume 11, Issue 5

Abstract: Several studies have strengthened the link between the gut microbiota (GM) and the response to immunotherapy in patients with tumors, highlighting the potential role of GM as a biomarker of response. Targeted therapies including B-cell receptor (BCR) ... ...

Abstract	Several studies have strengthened the link between the gut microbiota (GM) and the response to immunotherapy in patients with tumors, highlighting the potential role of GM as a biomarker of response. Targeted therapies including B-cell receptor (BCR) inhibitors (BCRi) represent the newest approach to the treatment of chronic lymphocytic leukemia (CLL); however, not all patients achieve a satisfactory response, and immune-related adverse events (irAEs) can also impact the efficacy. The aim of the study was to compare GM biodiversity in patients with CLL, treated with BCRi for at least 12 months. Twelve patients were enrolled: 10 patients in the
Language	English
Publishing date	2023-05-17
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2720891-6
ISSN	2076-2607
ISSN	2076-2607
DOI	10.3390/microorganisms11051305
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Article ; Online: Rapid spread of a novel NDM-producing clone of

Mileto, Irene / Petazzoni, Greta / Corbella, Marta / Gaiarsa, Stefano / Merla, Cristina / Kuka, Angela / Ramus, Marina / Terulla, Cristina / Brandolini, Micaela / Piralla, Antonio / Cambieri, Patrizia / Baldanti, Fausto

Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin

2023 Volume 28, Issue 42

Abstract: New Delhi metallo-beta-lactamase (NDM)- ... ...

Abstract	New Delhi metallo-beta-lactamase (NDM)-producing
MeSH term(s)	Humans ; Klebsiella pneumoniae/genetics ; Klebsiella Infections/drug therapy ; Klebsiella Infections/epidemiology ; beta-Lactamases/genetics ; Anti-Bacterial Agents/pharmacology ; Anti-Bacterial Agents/therapeutic use ; Disease Outbreaks ; Italy/epidemiology ; Microbial Sensitivity Tests
Chemical Substances	beta-Lactamases (EC 3.5.2.6) ; Anti-Bacterial Agents
Language	English
Publishing date	2023-10-19
Publishing country	Sweden
Document type	Journal Article
ZDB-ID	1338803-4
ISSN	1560-7917 ; 1025-496X
ISSN (online)	1560-7917
ISSN	1025-496X
DOI	10.2807/1560-7917.ES.2023.28.42.2300522
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Article ; Online: Reduction of BSI associated mortality after a sepsis project implementation in the ER of a tertiary referral hospital.

Seminari, Elena / Colaneri, Marta / Corbella, Marta / De Silvestri, Annalisa / Muzzi, Alba / Perlini, Stefano / Martino, Ilaria Francesca / Marvulli, Lea Nadia / Arcuri, Alessia / Maffezzoni, Marcello / Minucci, Rita / Bono, Enrica / Cambieri, Patrizia / Marone, Piero / Bruno, Raffaele

Scientific reports

2023 Volume 13, Issue 1, Page(s) 5142

Abstract: The emergency room (ER) is the first gateway for patients with sepsis to inpatient units, and identifying best practices and benchmarks to be applied in this setting might crucially result in better patient's outcomes. In this study, we want to evaluate ... ...

Abstract	The emergency room (ER) is the first gateway for patients with sepsis to inpatient units, and identifying best practices and benchmarks to be applied in this setting might crucially result in better patient's outcomes. In this study, we want to evaluate the results in terms of decreased the in-hospital mortality of patients with sepsis of a Sepsis Project developed in the ER. All patients admitted to the ER of our Hospital from the 1st January, 2016 to the 31stJuly 2019 with suspect of sepsis (MEWS score ≥ of 3) and positive blood culture upon ER admission were included in this retrospective observational study. The study comprises of two periods: Period A: From the 1st Jan 2016 to the 31st Dec 2017, before the implementation of the Sepsis project. Period B: From the 1st Jan 2018 to the 31stJul 2019, after the implementation of the Sepsis project. To analyze the difference in mortality between the two periods, a univariate and multivariate logistic regression was used. The risk of in-hospital mortality was expressed as an odds ratio (OR) and a 95% confidence interval (95% CI). Overall, 722 patients admitted in ER had positive BC on admissions, 408 in period A and 314 in period B. In-hospital mortality was 18.9% in period A and 12.7% in period B (p = 0.03). At multivariable analysis, mortality was still reduced in period B compared to period A (OR 0.64, 95% CI 0.41-0.98; p = 0.045). Having an infection due to GP bacteria or polymicrobial was associated with an increased risk of death, as it was having a neoplasm or diabetes. A marked reduction in in-hospital mortality of patients with documented BSI associated with signs or symptoms of sepsis after the implementation of a sepsis project based on the application of sepsis bundles in the ER.
MeSH term(s)	Humans ; Tertiary Care Centers ; Hospitalization ; Sepsis ; Retrospective Studies ; Hospital Mortality ; Emergency Service, Hospital
Language	English
Publishing date	2023-03-29
Publishing country	England
Document type	Observational Study ; Journal Article
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-023-31219-1
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