Sustained outbreak of blaVIM-1 harbouring pathogens in an Italian tertiary hospital: Genomic insights into persistence and spreading
•Genomic analysis reveals a prolonged outbreak of blaVIM-1 producing bacteria.•Hospital environment serves as a hidden reservoir for blaVIM-1 persistence.•A shared class 1 integron facilitates blaVIM-1 spread across multiple species.•Whole-genome sequencing reveals complex transmission dynamics in t...
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| Published in: | Journal of Global Antimicrobial Resistance Vol. 44; pp. 111 - 115 |
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| Main Authors: | , , , , , , , , |
| Format: | Journal Article |
| Language: | English |
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01.09.2025
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| ISSN: | 2213-7165, 2213-7173, 2213-7165 |
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| Abstract | •Genomic analysis reveals a prolonged outbreak of blaVIM-1 producing bacteria.•Hospital environment serves as a hidden reservoir for blaVIM-1 persistence.•A shared class 1 integron facilitates blaVIM-1 spread across multiple species.•Whole-genome sequencing reveals complex transmission dynamics in the outbreak.
We investigated an outbreak of blaVIM harbouring pathogens lasting over a year, affecting patients in an intensive care unit (ICU) in a tertiary hospital in Bergamo, Italy. To identify transmission routes of pathogens, we combined classical epidemiological investigation with the molecular identification of the mobile genetic elements (MGEs), integrons, and resistance cassettes that could have played a role in the outbreak persistence.
Short and long reads sequencing were performed. Transmission, resistome, and virulome analysis were conducted, as well as the identification of plasmids and integrons harbouring blaVIM-1.
Forty-four blaVIM harbouring isolates, including Enterobacterales and Pseudomonadaceae, were identified from patients and environmental samples. The strains exhibited diverse resistomes and virulomes, with high mortality rates among infected patients. The performed assembly analysis did not support the hypothesis of interspecies plasmid transmission, but, nonetheless, genomic analysis revealed a consistent presence of a class 1 integron (IntI1) in all the analysed strains. The identification of the same IntI1 in clinical and environmental samples suggests a potential reservoir for resistant strains in the hospital environment.
These findings emphasize the need for comprehensive infection control measures, including genomic-based surveillance, to address MGEs’ horizontal spreading and persistence in the healthcare setting. © 2025 The Author(s). Published by Elsevier Ltd on behalf of International Society for Antimicrobial Chemotherapy. |
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| AbstractList | We investigated an outbreak of blaVIM harbouring pathogens lasting over a year, affecting intensive care unit (ICU) patients in a tertiary hospital in Bergamo, Italy. To identify transmission routes of pathogens, we combined classical epidemiological investigation with the molecular identification of the mobile genetic elements (MGEs), integrons and resistance cassettes that could have played a role in the outbreak persistence.BACKGROUNDWe investigated an outbreak of blaVIM harbouring pathogens lasting over a year, affecting intensive care unit (ICU) patients in a tertiary hospital in Bergamo, Italy. To identify transmission routes of pathogens, we combined classical epidemiological investigation with the molecular identification of the mobile genetic elements (MGEs), integrons and resistance cassettes that could have played a role in the outbreak persistence.Short and long reads sequencing were performed. Transmission, resistome and virulome analysis were conducted, as well as the identification of plasmids and integrons harbouring blaVIM-1. RESULTS: Forty four blaVIM harbouring isolates, including Enterobacterales and Pseudomonadaceae, were identified from patients and environmental samples. The strains exhibited diverse resistomes and virulomes, with high mortality rates among infected patients. The performed assembly analysis did not support the hypothesis of interspecies plasmid transmission, nonetheless genomic analysis revealed a consistent presence of a Class 1 integron (IntI1) in all the analysed strains. The identification of the same IntI1 in clinical and environmental samples suggests a potential reservoir for resistant strains in the hospital environment.METHODSShort and long reads sequencing were performed. Transmission, resistome and virulome analysis were conducted, as well as the identification of plasmids and integrons harbouring blaVIM-1. RESULTS: Forty four blaVIM harbouring isolates, including Enterobacterales and Pseudomonadaceae, were identified from patients and environmental samples. The strains exhibited diverse resistomes and virulomes, with high mortality rates among infected patients. The performed assembly analysis did not support the hypothesis of interspecies plasmid transmission, nonetheless genomic analysis revealed a consistent presence of a Class 1 integron (IntI1) in all the analysed strains. The identification of the same IntI1 in clinical and environmental samples suggests a potential reservoir for resistant strains in the hospital environment.These findings emphasize the need for comprehensive infection control measures, including genomic-based surveillance, to address MGEs' horizontal spreading and persistence in the healthcare setting.CONCLUSIONSThese findings emphasize the need for comprehensive infection control measures, including genomic-based surveillance, to address MGEs' horizontal spreading and persistence in the healthcare setting. Objectives: We investigated an outbreak of blaVIM harbouring pathogens lasting over a year, affecting patients in an intensive care unit (ICU) in a tertiary hospital in Bergamo, Italy. To identify transmission routes of pathogens, we combined classical epidemiological investigation with the molecular identification of the mobile genetic elements (MGEs), integrons, and resistance cassettes that could have played a role in the outbreak persistence. Methods: Short and long reads sequencing were performed. Transmission, resistome, and virulome analysis were conducted, as well as the identification of plasmids and integrons harbouring blaVIM-1. Results: Forty-four blaVIM harbouring isolates, including Enterobacterales and Pseudomonadaceae, were identified from patients and environmental samples. The strains exhibited diverse resistomes and virulomes, with high mortality rates among infected patients. The performed assembly analysis did not support the hypothesis of interspecies plasmid transmission, but, nonetheless, genomic analysis revealed a consistent presence of a class 1 integron (IntI1) in all the analysed strains. The identification of the same IntI1 in clinical and environmental samples suggests a potential reservoir for resistant strains in the hospital environment. Conclusions: These findings emphasize the need for comprehensive infection control measures, including genomic-based surveillance, to address MGEs’ horizontal spreading and persistence in the healthcare setting. © 2025 The Author(s). Published by Elsevier Ltd on behalf of International Society for Antimicrobial Chemotherapy. •Genomic analysis reveals a prolonged outbreak of blaVIM-1 producing bacteria.•Hospital environment serves as a hidden reservoir for blaVIM-1 persistence.•A shared class 1 integron facilitates blaVIM-1 spread across multiple species.•Whole-genome sequencing reveals complex transmission dynamics in the outbreak. We investigated an outbreak of blaVIM harbouring pathogens lasting over a year, affecting patients in an intensive care unit (ICU) in a tertiary hospital in Bergamo, Italy. To identify transmission routes of pathogens, we combined classical epidemiological investigation with the molecular identification of the mobile genetic elements (MGEs), integrons, and resistance cassettes that could have played a role in the outbreak persistence. Short and long reads sequencing were performed. Transmission, resistome, and virulome analysis were conducted, as well as the identification of plasmids and integrons harbouring blaVIM-1. Forty-four blaVIM harbouring isolates, including Enterobacterales and Pseudomonadaceae, were identified from patients and environmental samples. The strains exhibited diverse resistomes and virulomes, with high mortality rates among infected patients. The performed assembly analysis did not support the hypothesis of interspecies plasmid transmission, but, nonetheless, genomic analysis revealed a consistent presence of a class 1 integron (IntI1) in all the analysed strains. The identification of the same IntI1 in clinical and environmental samples suggests a potential reservoir for resistant strains in the hospital environment. These findings emphasize the need for comprehensive infection control measures, including genomic-based surveillance, to address MGEs’ horizontal spreading and persistence in the healthcare setting. © 2025 The Author(s). Published by Elsevier Ltd on behalf of International Society for Antimicrobial Chemotherapy. |
| Author | Averara, Franca Cirillo, Daniela Maria Di Marco, Federico Moghaddasi, Kiarash Del Castillo, Gabriele Batignani, Virginia Bracco, Silvia Saluzzo, Francesca Farina, Claudio |
| Author_xml | – sequence: 1 givenname: Francesca orcidid: 0000-0001-6705-1716 surname: Saluzzo fullname: Saluzzo, Francesca organization: Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy – sequence: 2 givenname: Federico orcidid: 0000-0003-0376-1342 surname: Di Marco fullname: Di Marco, Federico organization: Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy – sequence: 3 givenname: Virginia surname: Batignani fullname: Batignani, Virginia organization: Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy – sequence: 4 givenname: Kiarash surname: Moghaddasi fullname: Moghaddasi, Kiarash organization: Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy – sequence: 5 givenname: Franca surname: Averara fullname: Averara, Franca organization: Department of Health Care Professions, ASST “Papa Giovanni XXIII”, Bergamo, Italy – sequence: 6 givenname: Silvia surname: Bracco fullname: Bracco, Silvia organization: Microbiology and Virology Laboratory, ASST “Papa Giovanni XXIII”, Bergamo, Italy – sequence: 7 givenname: Gabriele orcidid: 0000-0002-3331-2815 surname: Del Castillo fullname: Del Castillo, Gabriele organization: Health Care Coordination Offices, ASST “Papa Giovanni XXIII”, Bergamo, Italy – sequence: 8 givenname: Claudio orcidid: 0000-0003-2298-4293 surname: Farina fullname: Farina, Claudio organization: Microbiology and Virology Laboratory, ASST “Papa Giovanni XXIII”, Bergamo, Italy – sequence: 9 givenname: Daniela Maria orcidid: 0000-0001-6415-1535 surname: Cirillo fullname: Cirillo, Daniela Maria email: cirillo.daniela@hsr.it organization: Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy |
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| Cites_doi | 10.1093/bioinformatics/btt086 10.1128/CMR.00088-17 10.1186/s13059-021-02483-z 10.1186/s13059-019-1891-0 10.1038/s44259-024-00069-w 10.1007/s11908-018-0620-2 10.1371/journal.pcbi.1005595 10.1093/bioinformatics/btv271 10.1128/AAC.00483-19 10.1016/S1473-3099(19)30230-0 10.3390/microorganisms10040700 10.1016/j.scitotenv.2020.138248 10.1074/mcp.M116.060582 10.1007/s40121-020-00395-2 10.12688/f1000research.20887.2 10.1093/nar/gkv1239 10.1016/S0168-6496(03)00164-8 10.1128/AAC.02412-14 10.1093/cid/cix132 10.1128/JB.00152-08 10.7717/peerj-cs.104 10.1007/s11908-024-00836-w |
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| References | Schwengers, Jelonek, Dieckmann, Beyvers, Blom, Goesmann (bib0018) 2021; 7 Suleyman, Alangaden, Bardossy (bib0006) 2018; 20 Hansen (bib0023) 2021; 10 Gardner, Slezak, Hall (bib0015) 2015; 31 Gurevich, Saveliev, Vyahhi, Tesler (bib0011) 2013; 29 Lu, Breitwieser, Thielen, Salzberg (bib0009) 2017; 2017 Doll, Bryson, Palmore (bib0003) 2024; 26 Pettersen, Mosevoll, Lindemann, Wiker (bib0020) 2016; 15 Tennstedt, Szczepanowski, Braun, Pühler, Schlüter (bib0021) 2003; 45 Mathers, Li, He, Narendra, Stoesser, Eyre (bib0004) 2024; 2 Gillings, Boucher, Labbate, Holmes, Krishnan, Holley (bib0001) 2008; 190 Kizny Gordon, Mathers, Cheong, Gottlieb, Kotay, Walker (bib0005) 2017; 64 Smismans, Ho, Daniels, Ombelet, Mellaerts, Obbels (bib0007) 2019; 19 Néron, Littner, Haudiquet, Perrin, Cury, Rocha (bib0019) 2022; 10 Carattoli, Zankari, Garciá-Fernández, Larsen, Lund, Villa (bib0014) 2014; 58 Feldgarden, Brover, Haft, Prasad, Slotta, Tolstoy (bib0012) 2019; 63 Gustavsen, Pai, Isserlin, Demchak, Pico (bib0016) 2019; 8 Partridge, Kwong, Firth, Jensen (bib0002) 2018; 31 Wood, Lu, Langmead (bib0008) 2019; 20 Wick, Judd, Gorrie, Holt (bib0010) 2017; 13 Chen, Zheng, Liu, Yang, Jin (bib0013) 2016; 44 Wick, Judd, Cerdeira, Hawkey, Méric, Vezina (bib0017) 2021; 22 Zhang, Yang, Xiang, Xu, Zheng, Lu (bib0022) 2020; 724 Smismans (10.1016/j.jgar.2025.06.007_bib0007) 2019; 19 Wick (10.1016/j.jgar.2025.06.007_bib0017) 2021; 22 Zhang (10.1016/j.jgar.2025.06.007_bib0022) 2020; 724 Gustavsen (10.1016/j.jgar.2025.06.007_bib0016) 2019; 8 Pettersen (10.1016/j.jgar.2025.06.007_bib0020) 2016; 15 Schwengers (10.1016/j.jgar.2025.06.007_bib0018) 2021; 7 Wick (10.1016/j.jgar.2025.06.007_bib0010) 2017; 13 Néron (10.1016/j.jgar.2025.06.007_bib0019) 2022; 10 Kizny Gordon (10.1016/j.jgar.2025.06.007_bib0005) 2017; 64 Partridge (10.1016/j.jgar.2025.06.007_bib0002) 2018; 31 Mathers (10.1016/j.jgar.2025.06.007_bib0004) 2024; 2 Doll (10.1016/j.jgar.2025.06.007_bib0003) 2024; 26 Feldgarden (10.1016/j.jgar.2025.06.007_bib0012) 2019; 63 Gillings (10.1016/j.jgar.2025.06.007_bib0001) 2008; 190 Gardner (10.1016/j.jgar.2025.06.007_bib0015) 2015; 31 Tennstedt (10.1016/j.jgar.2025.06.007_bib0021) 2003; 45 Gurevich (10.1016/j.jgar.2025.06.007_bib0011) 2013; 29 Suleyman (10.1016/j.jgar.2025.06.007_bib0006) 2018; 20 Carattoli (10.1016/j.jgar.2025.06.007_bib0014) 2014; 58 Hansen (10.1016/j.jgar.2025.06.007_bib0023) 2021; 10 Lu (10.1016/j.jgar.2025.06.007_bib0009) 2017; 2017 Chen (10.1016/j.jgar.2025.06.007_bib0013) 2016; 44 Wood (10.1016/j.jgar.2025.06.007_bib0008) 2019; 20 |
| References_xml | – volume: 10 start-page: 75 year: 2021 end-page: 92 ident: bib0023 article-title: Continuous evolution: perspective on the epidemiology of carbapenemase resistance among enterobacterales and other gram-negative bacteria publication-title: Infect Dis Ther – volume: 58 start-page: 3895 year: 2014 end-page: 3903 ident: bib0014 article-title: In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing publication-title: Antimicrob Agents Chemother – volume: 31 year: 2018 ident: bib0002 article-title: Mobile genetic elements associated with antimicrobial resistance publication-title: Clin Microbiol Rev – volume: 29 start-page: 1072 year: 2013 end-page: 1075 ident: bib0011 article-title: QUAST: quality assessment tool for genome assemblies publication-title: Bioinformatics – volume: 20 start-page: 1 year: 2018 end-page: 11 ident: bib0006 article-title: The role of environmental contamination in the transmission of nosocomial pathogens and healthcare-associated infections publication-title: Curr Infect Dis Rep – volume: 13 year: 2017 ident: bib0010 article-title: Unicycler: resolving bacterial genome assemblies from short and long sequencing reads publication-title: PLoS Comput Biol – volume: 2017 start-page: e104 year: 2017 ident: bib0009 article-title: Bracken: estimating species abundance in metagenomics data publication-title: PeerJ Comput Sci – volume: 44 start-page: D694 year: 2016 end-page: D697 ident: bib0013 article-title: VFDB 2016: hierarchical and refined dataset for big data analysis–10 years on publication-title: Nucleic Acids Res – volume: 8 start-page: 1774 year: 2019 ident: bib0016 article-title: RCy3: network biology using Cytoscape from within R publication-title: F1000Res – volume: 10 start-page: 700 year: 2022 ident: bib0019 article-title: IntegronFinder 2.0: identification and analysis of integrons across bacteria, with a focus on antibiotic resistance in Klebsiella publication-title: Microorganisms – volume: 190 start-page: 5095 year: 2008 end-page: 5100 ident: bib0001 article-title: The evolution of class 1 integrons and the rise of antibiotic resistance publication-title: J Bacteriol – volume: 64 start-page: 1436 year: 2017 end-page: 1444 ident: bib0005 article-title: The hospital water environment as a reservoir for carbapenem-resistant organisms causing hospital-acquired infections - A systematic review of the literature publication-title: Clin Infect Dis – volume: 26 start-page: 115 year: 2024 end-page: 121 ident: bib0003 article-title: Whole genome sequencing applications in hospital epidemiology and infection prevention publication-title: Curr Infect Dis Rep – volume: 724 year: 2020 ident: bib0022 article-title: Evolutions of antibiotic resistance genes (ARGs), class 1 integron-integrase (intI1) and potential hosts of ARGs during sludge anaerobic digestion with the iron nanoparticles addition publication-title: Sci Total Environ – volume: 19 start-page: 580 year: 2019 end-page: 581 ident: bib0007 article-title: New environmental reservoir of CPE in hospitals publication-title: Lancet Infect Dis – volume: 20 start-page: 1 year: 2019 end-page: 13 ident: bib0008 article-title: Improved metagenomic analysis with Kraken 2 publication-title: Genome Biol – volume: 7 year: 2021 ident: bib0018 article-title: Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification publication-title: Microb Genom – volume: 63 year: 2019 ident: bib0012 article-title: Validating the AMRFinder tool and resistance gene database by using antimicrobial resistance genotype-phenotype correlations in a collection of isolates publication-title: Antimicrob Agents Chemother – volume: 45 start-page: 239 year: 2003 end-page: 252 ident: bib0021 article-title: Occurrence of integron-associated resistance gene cassettes located on antibiotic resistance plasmids isolated from a wastewater treatment plant publication-title: FEMS Microbiol Ecol – volume: 2 start-page: 50 year: 2024 ident: bib0004 article-title: Developing a framework for tracking antimicrobial resistance gene movement in a persistent environmental reservoir publication-title: NPJ Antimicrob Resist – volume: 22 start-page: 1 year: 2021 end-page: 17 ident: bib0017 article-title: Trycycler: consensus long-read assemblies for bacterial genomes publication-title: Genome Biol – volume: 15 start-page: 2890 year: 2016 ident: bib0020 article-title: Coordination of metabolism and virulence factors expression of extraintestinal pathogenic Escherichia coli purified from blood cultures of patients with sepsis publication-title: Mol Cell Proteomics – volume: 31 start-page: 2877 year: 2015 end-page: 2878 ident: bib0015 article-title: kSNP3.0: SNP detection and phylogenetic analysis of genomes without genome alignment or reference genome publication-title: Bioinformatics – volume: 29 start-page: 1072 year: 2013 ident: 10.1016/j.jgar.2025.06.007_bib0011 article-title: QUAST: quality assessment tool for genome assemblies publication-title: Bioinformatics doi: 10.1093/bioinformatics/btt086 – volume: 31 year: 2018 ident: 10.1016/j.jgar.2025.06.007_bib0002 article-title: Mobile genetic elements associated with antimicrobial resistance publication-title: Clin Microbiol Rev doi: 10.1128/CMR.00088-17 – volume: 22 start-page: 1 year: 2021 ident: 10.1016/j.jgar.2025.06.007_bib0017 article-title: Trycycler: consensus long-read assemblies for bacterial genomes publication-title: Genome Biol doi: 10.1186/s13059-021-02483-z – volume: 7 year: 2021 ident: 10.1016/j.jgar.2025.06.007_bib0018 article-title: Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification publication-title: Microb Genom – volume: 20 start-page: 1 year: 2019 ident: 10.1016/j.jgar.2025.06.007_bib0008 article-title: Improved metagenomic analysis with Kraken 2 publication-title: Genome Biol doi: 10.1186/s13059-019-1891-0 – volume: 2 start-page: 50 year: 2024 ident: 10.1016/j.jgar.2025.06.007_bib0004 article-title: Developing a framework for tracking antimicrobial resistance gene movement in a persistent environmental reservoir publication-title: NPJ Antimicrob Resist doi: 10.1038/s44259-024-00069-w – volume: 20 start-page: 1 year: 2018 ident: 10.1016/j.jgar.2025.06.007_bib0006 article-title: The role of environmental contamination in the transmission of nosocomial pathogens and healthcare-associated infections publication-title: Curr Infect Dis Rep doi: 10.1007/s11908-018-0620-2 – volume: 13 year: 2017 ident: 10.1016/j.jgar.2025.06.007_bib0010 article-title: Unicycler: resolving bacterial genome assemblies from short and long sequencing reads publication-title: PLoS Comput Biol doi: 10.1371/journal.pcbi.1005595 – volume: 31 start-page: 2877 year: 2015 ident: 10.1016/j.jgar.2025.06.007_bib0015 article-title: kSNP3.0: SNP detection and phylogenetic analysis of genomes without genome alignment or reference genome publication-title: Bioinformatics doi: 10.1093/bioinformatics/btv271 – volume: 63 year: 2019 ident: 10.1016/j.jgar.2025.06.007_bib0012 article-title: Validating the AMRFinder tool and resistance gene database by using antimicrobial resistance genotype-phenotype correlations in a collection of isolates publication-title: Antimicrob Agents Chemother doi: 10.1128/AAC.00483-19 – volume: 19 start-page: 580 year: 2019 ident: 10.1016/j.jgar.2025.06.007_bib0007 article-title: New environmental reservoir of CPE in hospitals publication-title: Lancet Infect Dis doi: 10.1016/S1473-3099(19)30230-0 – volume: 10 start-page: 700 year: 2022 ident: 10.1016/j.jgar.2025.06.007_bib0019 article-title: IntegronFinder 2.0: identification and analysis of integrons across bacteria, with a focus on antibiotic resistance in Klebsiella publication-title: Microorganisms doi: 10.3390/microorganisms10040700 – volume: 724 year: 2020 ident: 10.1016/j.jgar.2025.06.007_bib0022 article-title: Evolutions of antibiotic resistance genes (ARGs), class 1 integron-integrase (intI1) and potential hosts of ARGs during sludge anaerobic digestion with the iron nanoparticles addition publication-title: Sci Total Environ doi: 10.1016/j.scitotenv.2020.138248 – volume: 15 start-page: 2890 year: 2016 ident: 10.1016/j.jgar.2025.06.007_bib0020 article-title: Coordination of metabolism and virulence factors expression of extraintestinal pathogenic Escherichia coli purified from blood cultures of patients with sepsis publication-title: Mol Cell Proteomics doi: 10.1074/mcp.M116.060582 – volume: 10 start-page: 75 year: 2021 ident: 10.1016/j.jgar.2025.06.007_bib0023 article-title: Continuous evolution: perspective on the epidemiology of carbapenemase resistance among enterobacterales and other gram-negative bacteria publication-title: Infect Dis Ther doi: 10.1007/s40121-020-00395-2 – volume: 8 start-page: 1774 year: 2019 ident: 10.1016/j.jgar.2025.06.007_bib0016 article-title: RCy3: network biology using Cytoscape from within R publication-title: F1000Res doi: 10.12688/f1000research.20887.2 – volume: 44 start-page: D694 year: 2016 ident: 10.1016/j.jgar.2025.06.007_bib0013 article-title: VFDB 2016: hierarchical and refined dataset for big data analysis–10 years on publication-title: Nucleic Acids Res doi: 10.1093/nar/gkv1239 – volume: 45 start-page: 239 year: 2003 ident: 10.1016/j.jgar.2025.06.007_bib0021 article-title: Occurrence of integron-associated resistance gene cassettes located on antibiotic resistance plasmids isolated from a wastewater treatment plant publication-title: FEMS Microbiol Ecol doi: 10.1016/S0168-6496(03)00164-8 – volume: 58 start-page: 3895 year: 2014 ident: 10.1016/j.jgar.2025.06.007_bib0014 article-title: In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing publication-title: Antimicrob Agents Chemother doi: 10.1128/AAC.02412-14 – volume: 64 start-page: 1436 year: 2017 ident: 10.1016/j.jgar.2025.06.007_bib0005 article-title: The hospital water environment as a reservoir for carbapenem-resistant organisms causing hospital-acquired infections - A systematic review of the literature publication-title: Clin Infect Dis doi: 10.1093/cid/cix132 – volume: 190 start-page: 5095 year: 2008 ident: 10.1016/j.jgar.2025.06.007_bib0001 article-title: The evolution of class 1 integrons and the rise of antibiotic resistance publication-title: J Bacteriol doi: 10.1128/JB.00152-08 – volume: 2017 start-page: e104 year: 2017 ident: 10.1016/j.jgar.2025.06.007_bib0009 article-title: Bracken: estimating species abundance in metagenomics data publication-title: PeerJ Comput Sci doi: 10.7717/peerj-cs.104 – volume: 26 start-page: 115 year: 2024 ident: 10.1016/j.jgar.2025.06.007_bib0003 article-title: Whole genome sequencing applications in hospital epidemiology and infection prevention publication-title: Curr Infect Dis Rep doi: 10.1007/s11908-024-00836-w |
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| SubjectTerms | Antimicrobial resistance Class 1 integrons Enterobacterales Genomic surveillance VIM |
| Title | Sustained outbreak of blaVIM-1 harbouring pathogens in an Italian tertiary hospital: Genomic insights into persistence and spreading |
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