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Article ; Online: Enterobacter asburiae ST229: an emerging carbapenemases producer.

Mattioni Marchetti, Vittoria / Kuka, Angela / Piazza, Aurora / Gaiarsa, Stefano / Merla, Cristina / Sottosanti, Mariangela / Cambieri, Patrizia / Migliavacca, Roberta / Baldanti, Fausto

Scientific reports

2024 Volume 14, Issue 1, Page(s) 6220

Abstract: Enterobacter asburiae, member of the Enterobacter cloacae complex (ECC) group, shows an increasing clinical relevance being responsible for infections like pneumonia, urinary tract infections and septicemia. The aim of the present study was the ... ...

Abstract	Enterobacter asburiae, member of the Enterobacter cloacae complex (ECC) group, shows an increasing clinical relevance being responsible for infections like pneumonia, urinary tract infections and septicemia. The aim of the present study was the investigation of the genomic features of two XDR E. asburiae ST229 clinical strains co-carrying blaNDM-1 and blaVIM-1 determinants, collected in October 2021 and in June 2022, respectively. Two E. asburiae strains were collected from rectal swabs of as many patients admitted to the cardiopulmonary intensive care unit of Fondazione I.R.C.C.S. "Policlinico San Matteo" in Pavia, Italy. Based on the antibiotic susceptibility profile results, both isolates showed an XDR phenotype, retaining susceptibility only to fluoroquinolones. Both isolates shared identical resistome, virulome, plasmid content, and belonged to ST229, a rarely reported sequence type. They co-harbored blaNDM-1 and blaVIM-1 genes, that resulted located on transferable plasmids by conjugation and transformation. Moreover, both strains differed in 24 SNPs and showed genetic relatedness with E. asburiae ST709 and ST27. We described the first case of ST229 E. asburiae co-harboring blaNDM-1 and blaVIM-1 in Italy. This study points out the emergence of carbapenemases in low-risk pathogens, representing a novel challenge for public health, that should include such types of strains in dedicated surveillance programs. Antimicrobial susceptibility testing was carried out using Thermo Scientific™ Sensititre™ Gram Negative MIC Plates DKMGN. Both strains underwent whole-genome sequencing (WGS) using Illumina Miseq platform. Resistome, plasmidome, virulome, MLST, plasmid MLST and a SNPs-based phylogenetic tree were in silico determined.
MeSH term(s)	Humans ; Anti-Bacterial Agents/pharmacology ; Multilocus Sequence Typing ; Phylogeny ; Bacterial Proteins ; beta-Lactamases ; Enterobacter
Chemical Substances	carbapenemase (EC 3.5.2.6) ; Anti-Bacterial Agents ; Bacterial Proteins ; beta-Lactamases (EC 3.5.2.6)
Language	English
Publishing date	2024-03-14
Publishing country	England
Document type	Case Reports ; Journal Article
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-024-55884-y
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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: P-DOR, an easy-to-use pipeline to reconstruct bacterial outbreaks using genomics.

Batisti Biffignandi, Gherard / Bellinzona, Greta / Petazzoni, Greta / Sassera, Davide / Zuccotti, Gian Vincenzo / Bandi, Claudio / Baldanti, Fausto / Comandatore, Francesco / Gaiarsa, Stefano

Bioinformatics (Oxford, England)

2023 Volume 39, Issue 9

Abstract: Summary: Bacterial Healthcare-Associated Infections (HAIs) are a major threat worldwide, which can be counteracted by establishing effective infection control measures, guided by constant surveillance and timely epidemiological investigations. Genomics ... ...

Abstract	Summary: Bacterial Healthcare-Associated Infections (HAIs) are a major threat worldwide, which can be counteracted by establishing effective infection control measures, guided by constant surveillance and timely epidemiological investigations. Genomics is crucial in modern epidemiology but lacks standard methods and user-friendly software, accessible to users without a strong bioinformatics proficiency. To overcome these issues we developed P-DOR, a novel tool for rapid bacterial outbreak characterization. P-DOR accepts genome assemblies as input, it automatically selects a background of publicly available genomes using k-mer distances and adds it to the analysis dataset before inferring a Single-Nucleotide Polymorphism (SNP)-based phylogeny. Epidemiological clusters are identified considering the phylogenetic tree topology and SNP distances. By analyzing the SNP-distance distribution, the user can gauge the correct threshold. Patient metadata can be inputted as well, to provide a spatio-temporal representation of the outbreak. The entire pipeline is fast and scalable and can be also run on low-end computers. Availability and implementation: P-DOR is implemented in Python3 and R and can be installed using conda environments. It is available from GitHub https://github.com/SteMIDIfactory/P-DOR under the GPL-3.0 license.
MeSH term(s)	Humans ; Phylogeny ; Genomics/methods ; Computational Biology/methods ; Genome ; Software ; Bacteria ; Disease Outbreaks ; Genome, Bacterial
Language	English
Publishing date	2023-09-27
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1422668-6
ISSN	1367-4811 ; 1367-4803
ISSN (online)	1367-4811
ISSN	1367-4803
DOI	10.1093/bioinformatics/btad571
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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: Spread of multiple SARS-CoV-2 lineages April-August 2020 anticipated the second pandemic wave in Lombardy (Italy).

Tallarita, Monica / Giardina, Federica / Novazzi, Federica / Gaiarsa, Stefano / Batisti Biffignandi, Gherard / Paolucci, Stefania / Rovida, Francesca / Piralla, Antonio / Baldanti, Fausto

Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology

2022 Volume 33 Suppl 27, Page(s) 89–92

Abstract: During the early phase of the pandemic (20 February-4 April 2020), we have investigated the temporal and geographical evolution of the virus in Lombardy showing the circulation of at least seven lineages distributed differently in the Region. In the ... ...

Abstract	During the early phase of the pandemic (20 February-4 April 2020), we have investigated the temporal and geographical evolution of the virus in Lombardy showing the circulation of at least seven lineages distributed differently in the Region. In the present study, the molecular epidemiology of SARS-CoV-2 was monitored in a period between two pandemic waves in order to track the circulation of new variants (April-August 2020). A great majority of SARS-CoV-2 strains (70.8%) belonged to lineages B, B.1, B.1.1 and B.1.1.1, and five strains belonging to four lineages were already reported in Italy (B.1.1.148, B.1.1.162, B.1.1.71, and B.1.425). In addition, 21 SARS-CoV-2 strains belonged to six lineages not previously observed in Italy were detected. No variants of concern were observed. A total of 152/1274 (11.3%) amino acid changes were observed among spike gene sequences and only 26/152 (17.1%) occurred in the receptor-binding domain region of the spike protein. Results of this study are indicative of ongoing transmission throughout the lockdown period, rather than re-introduction of novel lineages past lockdown. The use of molecular epidemiology in Italy should be promoted in order to provide additional understanding of the transmission of the disease and to have major effect on controlling the spread of disease.
MeSH term(s)	COVID-19 ; Communicable Disease Control ; Humans ; Italy/epidemiology ; Pandemics ; Phylogeny ; SARS-CoV-2
Language	English
Publishing date	2022-02-10
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1057059-7
ISSN	1399-3038 ; 0905-6157 ; 0906-5784
ISSN (online)	1399-3038
ISSN	0905-6157 ; 0906-5784
DOI	10.1111/pai.13641
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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: Concomitant Resistance to Cefiderocol and Ceftazidime/Avibactam in Two Carbapenemase-Producing

Bellinzona, Greta / Merla, Cristina / Corbella, Marta / Iskandar, Elizabeth Nagy / Seminari, Elena / Di Matteo, Angela / Gaiarsa, Stefano / Petazzoni, Greta / Sassera, Davide / Baldanti, Fausto / Piazza, Aurora / Cambieri, Patrizia

Microbial drug resistance (Larchmont, N.Y.)

2023 Volume 30, Issue 1, Page(s) 21–26

Abstract: In this study, we present two cases ... ...

Abstract	In this study, we present two cases of
MeSH term(s)	Humans ; Ceftazidime/pharmacology ; Ceftazidime/therapeutic use ; Anti-Bacterial Agents/pharmacology ; Klebsiella pneumoniae/genetics ; Cefiderocol ; Klebsiella Infections/drug therapy ; Microbial Sensitivity Tests ; beta-Lactamases/genetics ; Bacterial Proteins/genetics ; Azabicyclo Compounds/pharmacology ; Azabicyclo Compounds/therapeutic use ; Drug Combinations ; Carbapenem-Resistant Enterobacteriaceae
Chemical Substances	Ceftazidime (9M416Z9QNR) ; carbapenemase (EC 3.5.2.6) ; Anti-Bacterial Agents ; Cefiderocol (SZ34OMG6E8) ; avibactam (7352665165) ; beta-Lactamases (EC 3.5.2.6) ; Bacterial Proteins ; Azabicyclo Compounds ; Drug Combinations
Language	English
Publishing date	2023-10-23
Publishing country	United States
Document type	Journal Article
ZDB-ID	1290490-9
ISSN	1931-8448 ; 1076-6294
ISSN (online)	1931-8448
ISSN	1076-6294
DOI	10.1089/mdr.2023.0054
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Article ; Online: Comparative analysis of SARS-CoV-2 quasispecies in the upper and lower respiratory tract shows an ongoing evolution in the spike cleavage site.

Gaiarsa, Stefano / Giardina, Federica / Batisti Biffignandi, Gherard / Ferrari, Guglielmo / Piazza, Aurora / Tallarita, Monica / Novazzi, Federica / Bandi, Claudio / Paolucci, Stefania / Rovida, Francesca / Campanini, Giulia / Piralla, Antonio / Baldanti, Fausto

Virus research

2022 Volume 315, Page(s) 198786

Abstract: Studies are needed to better understand the genomic evolution of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This study aimed to describe viral quasispecies population of upper and lower respiratory tract by next-generation ... ...

Abstract	Studies are needed to better understand the genomic evolution of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This study aimed to describe viral quasispecies population of upper and lower respiratory tract by next-generation sequencing in patients admitted to intensive care unit. A deep sequencing of the S gene of SARS-CoV-2 from 109 clinical specimens, sampled from the upper respiratory tract (URT) and lower respiratory tract (LRT) of 77 patients was performed. A higher incidence of non-synonymous mutations and indels was observed in the LRT among minority variants. This might be explained by the ability of the virus to invade cells without interacting with ACE2 (e.g. exploiting macrophage phagocytosis). Minority variants are highly concentrated around the gene portion encoding for the Spike cleavage site, with a higher incidence in the URT; four mutations are highly recurring among samples and were found associated with the URT. Interestingly, 55.8% of minority variants detected in this locus were T>G and G>T transversions. Results from this study evidenced the presence of selective pressure and suggest that an evolutionary process is still ongoing in one of the crucial sites of spike protein associated with the spillover to humans.
MeSH term(s)	COVID-19 ; High-Throughput Nucleotide Sequencing ; Humans ; Quasispecies ; Respiratory System ; SARS-CoV-2/genetics ; Spike Glycoprotein, Coronavirus/genetics ; Spike Glycoprotein, Coronavirus/metabolism
Chemical Substances	Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2
Language	English
Publishing date	2022-04-14
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	605780-9
ISSN	1872-7492 ; 0168-1702
ISSN (online)	1872-7492
ISSN	0168-1702
DOI	10.1016/j.virusres.2022.198786
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