1
|
Analysis of Whole-Genome Sequences of Pathogenic Gram-Positive and Gram-Negative Isolates from the Same Hospital Environment to Investigate Common Evolutionary Trends Associated with Horizontal Gene Exchange, Mutations and DNA Methylation Patterning. Microorganisms 2023; 11:microorganisms11020323. [PMID: 36838287 PMCID: PMC9961978 DOI: 10.3390/microorganisms11020323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 01/05/2023] [Accepted: 01/09/2023] [Indexed: 01/31/2023] Open
Abstract
Hospital-acquired infections are a generally recognized problem for healthcare professionals. Clinical variants of Gram-negative and Gram-positive pathogens are characterized with enhanced antibiotic resistance and virulence due to mutations and the horizontal acquisition of respective genetic determinants. In this study, two Escherichia coli, two Klebsiella pneumoniae, three Pseudomonas aeruginosa, two Staphylococcus aureus, one Staphylococcus epidermidis and one Streptococcus pneumoniae showing broad spectra of antibiotic resistance were isolated from patients suffering from nosocomial infections in a local hospital in Almaty, Kazakhstan. The aim of the study was to compare general and species-specific pathways of the development of virulence and antibiotic resistance through opportunistic pathogens causing hospital-acquired infections. The whole-genome PacBio sequencing of the isolates allowed for the genotyping and identification of antibiotic resistance and virulence genetic determinants located in the chromosomes, plasmids and genomic islands. It was concluded that long-read sequencing is a useful tool for monitoring the epidemiological situation in hospitals. Marker antibiotic resistance mutations common for different microorganisms were identified, which were acquired due to antibiotic-selective pressure in the same clinical environment. The genotyping and identification of strain-specific DNA methylation motifs were found to be promising in estimating the risks associated with hospital infection outbreaks and monitoring the distribution and evolution of nosocomial pathogens.
Collapse
|
2
|
Montrucchio G, Costamagna A, Pierani T, Petitti A, Sales G, Pivetta E, Corcione S, Curtoni A, Cavallo R, De Rosa FG, Brazzi L. Bloodstream Infections Caused by Carbapenem-Resistant Pathogens in Intensive Care Units: Risk Factors Analysis and Proposal of a Prognostic Score. Pathogens 2022; 11:pathogens11070718. [PMID: 35889963 PMCID: PMC9315650 DOI: 10.3390/pathogens11070718] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/20/2022] [Accepted: 06/22/2022] [Indexed: 02/06/2023] Open
Abstract
Considering the growing prevalence of carbapenem-resistant Gram-negative bacteria (CR-GNB) bloodstream infection (BSI) in intensive care units (ICUs), the identification of specific risk factors and the development of a predictive model allowing for the early identification of patients at risk for CR-Klebsiella pneumoniae, Acinetobacter baumannii or Pseudomonas aeruginosa are essential. In this retrospective case–control study including all consecutive patients showing an episode of BSI in the ICUs of a university hospital in Italy in the period January–December 2016, patients with blood culture positive for CR-GNB pathogens and for any other bacteria were compared. A total of 106 patients and 158 episodes of BSI were identified. CR-GNBs induced BSI in 49 patients (46%) and 58 episodes (37%). Prognosis score and disease severity at admission, parenteral nutrition, cardiovascular surgery prior to admission to ICU, the presence of sepsis and septic shock, ventilation-associated pneumonia and colonization of the urinary or intestinal tract were statistically significant in the univariate analysis. The duration of ventilation and mortality at 28 days were significantly higher among CR-GNB cases. The prognostic model based on age, presence of sepsis, previous cardiovascular surgery, SAPS II, rectal colonization and invasive respiratory infection from the same pathogen showed a C-index of 89.6%. The identified risk factors are in line with the international literature. The proposal prognostic model seems easy to use and shows excellent performance but requires further studies to be validated.
Collapse
Affiliation(s)
- Giorgia Montrucchio
- Department of Surgical Sciences, University of Turin, 10126 Turin, Italy; (A.C.); (T.P.); (A.P.); (G.S.); (L.B.)
- Department of Anesthesia, Intensive Care and Emergency, Città Della Salute e Della Scienza di Torino University Hospital, 10126 Turin, Italy
- Correspondence:
| | - Andrea Costamagna
- Department of Surgical Sciences, University of Turin, 10126 Turin, Italy; (A.C.); (T.P.); (A.P.); (G.S.); (L.B.)
- Department of Anesthesia, Intensive Care and Emergency, Città Della Salute e Della Scienza di Torino University Hospital, 10126 Turin, Italy
| | - Tommaso Pierani
- Department of Surgical Sciences, University of Turin, 10126 Turin, Italy; (A.C.); (T.P.); (A.P.); (G.S.); (L.B.)
- Department of Anesthesia, Intensive Care and Emergency, Città Della Salute e Della Scienza di Torino University Hospital, 10126 Turin, Italy
| | - Alessandra Petitti
- Department of Surgical Sciences, University of Turin, 10126 Turin, Italy; (A.C.); (T.P.); (A.P.); (G.S.); (L.B.)
- Department of Anesthesia, Intensive Care and Emergency, Città Della Salute e Della Scienza di Torino University Hospital, 10126 Turin, Italy
| | - Gabriele Sales
- Department of Surgical Sciences, University of Turin, 10126 Turin, Italy; (A.C.); (T.P.); (A.P.); (G.S.); (L.B.)
- Department of Anesthesia, Intensive Care and Emergency, Città Della Salute e Della Scienza di Torino University Hospital, 10126 Turin, Italy
| | - Emanuele Pivetta
- Department of General and Specialized Medicine, Division of Emergency Medicine and High Dependency Unit, Città Della Salute e Della Scienza di Torino University Hospital, 10126 Turin, Italy;
| | - Silvia Corcione
- Department of Medical Sciences, Infectious Diseases, University of Turin, 10126 Turin, Italy; (S.C.); (F.G.D.R.)
- Division of Geographic Medicine, Tufts University School of Medicine, 145 Harrison Ave, Boston, MA 02111, USA
| | - Antonio Curtoni
- Microbiology and Virology Unit, Città Della Salute e Della Scienza di Torino University Hospital, 10126 Turin, Italy; (A.C.); (R.C.)
| | - Rossana Cavallo
- Microbiology and Virology Unit, Città Della Salute e Della Scienza di Torino University Hospital, 10126 Turin, Italy; (A.C.); (R.C.)
| | - Francesco Giuseppe De Rosa
- Department of Medical Sciences, Infectious Diseases, University of Turin, 10126 Turin, Italy; (S.C.); (F.G.D.R.)
| | - Luca Brazzi
- Department of Surgical Sciences, University of Turin, 10126 Turin, Italy; (A.C.); (T.P.); (A.P.); (G.S.); (L.B.)
- Department of Anesthesia, Intensive Care and Emergency, Città Della Salute e Della Scienza di Torino University Hospital, 10126 Turin, Italy
| |
Collapse
|