Multidrug-Resistant <i>Klebsiella pneumoniae</i> Strains in a Hospital: Phylogenetic Analysis to Investigate Local Epidemiology
Multidrug-resistant <i>Klebsiella pneumoniae</i> is a significant healthcare challenge that particularly affects vulnerable patients through opportunistic nosocomial infections. Surveillance is crucial for monitoring the prevalence of these infections. Eighty-four KPC <i>K. pneumon...
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2024-12-01
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| author | Maria Vittoria Ristori Fabio Scarpa Daria Sanna Marco Casu Nicola Petrosillo Umile Giuseppe Longo De Florio Lucia Silvia Spoto Rosa Maria Chiantia Alessandro Caserta Raffaella Rosy Vescio Flavio Davini Lucrezia Bani Elisabetta Riva Massimo Ciccozzi Silvia Angeletti |
| author_facet | Maria Vittoria Ristori Fabio Scarpa Daria Sanna Marco Casu Nicola Petrosillo Umile Giuseppe Longo De Florio Lucia Silvia Spoto Rosa Maria Chiantia Alessandro Caserta Raffaella Rosy Vescio Flavio Davini Lucrezia Bani Elisabetta Riva Massimo Ciccozzi Silvia Angeletti |
| author_sort | Maria Vittoria Ristori |
| collection | DOAJ |
| description | Multidrug-resistant <i>Klebsiella pneumoniae</i> is a significant healthcare challenge that particularly affects vulnerable patients through opportunistic nosocomial infections. Surveillance is crucial for monitoring the prevalence of these infections. Eighty-four KPC <i>K. pneumoniae</i> strains (2019–2022) were collected from patients admitted in Fondazione Policlinico Universitario Campus Bio-Medico. Strains were identified by MALDI-TOF and tested for antimicrobial susceptibility, and gene amplification was performed to identify the different blaKPC variants. Phylogenetic reconstructions were carried out using Bayesian methods. Additionally, to create a Bayesian skyline plot (BSP), additional analyses were conducted, running a simulation of 100 million generations under a Bayesian skyline model along with the uncorrelated log-normal relaxed clock model. To identify potential subgroups within genetic clusters and evaluate genetic variability among sequences, principal coordinate analysis (PCoA) was performed. In total, 84 <i>Klebsiella pneumoniae</i> isolates were classified as multidrug-resistant (MDR), characterized by resistance to three or more antibiotic classes, including carbapenems, and testing positive for KPC gene presence, and were included in the study. The Bayesian evolutionary tree for <i>K. pneumoniae</i> showed strongly supported branches but no genetic structure related to sampling dates or hospital departments. Phylogenetic analysis revealing a 73-year evolutionary span of <i>K. pneumoniae</i> strains. PCoA analysis identified three genetic outliers from 2022 and one from 2021, indicating higher genetic distances. The Bayesian skyline plot revealed increased genetic variability peaking at the end of 2019, followed by stabilization from early 2020 onward, with no significant changes in genetic variability thereafter. Overall, the study found no genetic structure correlating with sampling date or hospital department, suggesting significant variability in pathogen introduction during the pandemic. The increase in multidrug-resistant <i>K. pneumoniae</i> was linked to the influx of severe COVID-19 cases, prolonged hospitalizations, and heightened broad-spectrum antibiotic use, which likely facilitated resistance development and transmission amidst altered infection control practices. |
| format | Article |
| id | doaj-art-e46234f4da174132abbf66463827fecd |
| institution | DOAJ |
| issn | 2076-2607 |
| language | English |
| publishDate | 2024-12-01 |
| publisher | MDPI AG |
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| series | Microorganisms |
| spelling | doaj-art-e46234f4da174132abbf66463827fecd2025-08-20T02:43:43ZengMDPI AGMicroorganisms2076-26072024-12-011212254110.3390/microorganisms12122541Multidrug-Resistant <i>Klebsiella pneumoniae</i> Strains in a Hospital: Phylogenetic Analysis to Investigate Local EpidemiologyMaria Vittoria Ristori0Fabio Scarpa1Daria Sanna2Marco Casu3Nicola Petrosillo4Umile Giuseppe Longo5De Florio Lucia6Silvia Spoto7Rosa Maria Chiantia8Alessandro Caserta9Raffaella Rosy Vescio10Flavio Davini11Lucrezia Bani12Elisabetta Riva13Massimo Ciccozzi14Silvia Angeletti15Operative Research Unit of Laboratory, Fondazione Policlinico Universitario Campus Bio-Medico, Via Alvaro del Portillo, 200, 00128 Rome, ItalyDepartment of Biomedical Sciences, University of Sassari, Viale San Pietro 43b, 07100 Sassari, ItalyDepartment of Biomedical Sciences, University of Sassari, Viale San Pietro 43b, 07100 Sassari, ItalyDepartment of Veterinary Medicine, University of Sassari, 07100 Sassari, ItalyInfection Prevention Control and Infectious Disease Service, Fondazione Policlinico Universitario Campus Bio-Medico, 00128 Rome, ItalyFondazione Policlinico Universitario Campus Bio-Medico, Via Alvaro del Portillo, 200, 00128 Rome, ItalyOperative Research Unit of Laboratory, Fondazione Policlinico Universitario Campus Bio-Medico, Via Alvaro del Portillo, 200, 00128 Rome, ItalyDiagnostic and Therapeutic Medicine Department, Fondazione Policlinico Universitario Campus Bio-Medico, Via Alvaro del Portillo, 200, 00128 Roma, ItalyOperative Research Unit of Laboratory, Fondazione Policlinico Universitario Campus Bio-Medico, Via Alvaro del Portillo, 200, 00128 Rome, ItalyOperative Research Unit of Laboratory, Fondazione Policlinico Universitario Campus Bio-Medico, Via Alvaro del Portillo, 200, 00128 Rome, ItalyOperative Research Unit of Laboratory, Fondazione Policlinico Universitario Campus Bio-Medico, Via Alvaro del Portillo, 200, 00128 Rome, ItalyOperative Research Unit of Laboratory, Fondazione Policlinico Universitario Campus Bio-Medico, Via Alvaro del Portillo, 200, 00128 Rome, ItalyOperative Research Unit of Laboratory, Fondazione Policlinico Universitario Campus Bio-Medico, Via Alvaro del Portillo, 200, 00128 Rome, ItalyOperative Research Unit of Laboratory, Fondazione Policlinico Universitario Campus Bio-Medico, Via Alvaro del Portillo, 200, 00128 Rome, ItalyOperative Research Unit of Laboratory, Fondazione Policlinico Universitario Campus Bio-Medico, Via Alvaro del Portillo, 200, 00128 Rome, ItalyOperative Research Unit of Laboratory, Fondazione Policlinico Universitario Campus Bio-Medico, Via Alvaro del Portillo, 200, 00128 Rome, ItalyMultidrug-resistant <i>Klebsiella pneumoniae</i> is a significant healthcare challenge that particularly affects vulnerable patients through opportunistic nosocomial infections. Surveillance is crucial for monitoring the prevalence of these infections. Eighty-four KPC <i>K. pneumoniae</i> strains (2019–2022) were collected from patients admitted in Fondazione Policlinico Universitario Campus Bio-Medico. Strains were identified by MALDI-TOF and tested for antimicrobial susceptibility, and gene amplification was performed to identify the different blaKPC variants. Phylogenetic reconstructions were carried out using Bayesian methods. Additionally, to create a Bayesian skyline plot (BSP), additional analyses were conducted, running a simulation of 100 million generations under a Bayesian skyline model along with the uncorrelated log-normal relaxed clock model. To identify potential subgroups within genetic clusters and evaluate genetic variability among sequences, principal coordinate analysis (PCoA) was performed. In total, 84 <i>Klebsiella pneumoniae</i> isolates were classified as multidrug-resistant (MDR), characterized by resistance to three or more antibiotic classes, including carbapenems, and testing positive for KPC gene presence, and were included in the study. The Bayesian evolutionary tree for <i>K. pneumoniae</i> showed strongly supported branches but no genetic structure related to sampling dates or hospital departments. Phylogenetic analysis revealing a 73-year evolutionary span of <i>K. pneumoniae</i> strains. PCoA analysis identified three genetic outliers from 2022 and one from 2021, indicating higher genetic distances. The Bayesian skyline plot revealed increased genetic variability peaking at the end of 2019, followed by stabilization from early 2020 onward, with no significant changes in genetic variability thereafter. Overall, the study found no genetic structure correlating with sampling date or hospital department, suggesting significant variability in pathogen introduction during the pandemic. The increase in multidrug-resistant <i>K. pneumoniae</i> was linked to the influx of severe COVID-19 cases, prolonged hospitalizations, and heightened broad-spectrum antibiotic use, which likely facilitated resistance development and transmission amidst altered infection control practices.https://www.mdpi.com/2076-2607/12/12/2541<i>Klebsiella pneumoniae</i>MDRphylogenetic analysisepidemiology investigation |
| spellingShingle | Maria Vittoria Ristori Fabio Scarpa Daria Sanna Marco Casu Nicola Petrosillo Umile Giuseppe Longo De Florio Lucia Silvia Spoto Rosa Maria Chiantia Alessandro Caserta Raffaella Rosy Vescio Flavio Davini Lucrezia Bani Elisabetta Riva Massimo Ciccozzi Silvia Angeletti Multidrug-Resistant <i>Klebsiella pneumoniae</i> Strains in a Hospital: Phylogenetic Analysis to Investigate Local Epidemiology Microorganisms <i>Klebsiella pneumoniae</i> MDR phylogenetic analysis epidemiology investigation |
| title | Multidrug-Resistant <i>Klebsiella pneumoniae</i> Strains in a Hospital: Phylogenetic Analysis to Investigate Local Epidemiology |
| title_full | Multidrug-Resistant <i>Klebsiella pneumoniae</i> Strains in a Hospital: Phylogenetic Analysis to Investigate Local Epidemiology |
| title_fullStr | Multidrug-Resistant <i>Klebsiella pneumoniae</i> Strains in a Hospital: Phylogenetic Analysis to Investigate Local Epidemiology |
| title_full_unstemmed | Multidrug-Resistant <i>Klebsiella pneumoniae</i> Strains in a Hospital: Phylogenetic Analysis to Investigate Local Epidemiology |
| title_short | Multidrug-Resistant <i>Klebsiella pneumoniae</i> Strains in a Hospital: Phylogenetic Analysis to Investigate Local Epidemiology |
| title_sort | multidrug resistant i klebsiella pneumoniae i strains in a hospital phylogenetic analysis to investigate local epidemiology |
| topic | <i>Klebsiella pneumoniae</i> MDR phylogenetic analysis epidemiology investigation |
| url | https://www.mdpi.com/2076-2607/12/12/2541 |
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