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Gondal AJ, Choudhry N, Niaz A, Yasmin N. Molecular Analysis of Carbapenem and Aminoglycoside Resistance Genes in Carbapenem-Resistant Pseudomonas aeruginosa Clinical Strains: A Challenge for Tertiary Care Hospitals. Antibiotics (Basel) 2024; 13:191. [PMID: 38391577 PMCID: PMC10886086 DOI: 10.3390/antibiotics13020191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Revised: 01/09/2024] [Accepted: 01/23/2024] [Indexed: 02/24/2024] Open
Abstract
Carbapenem-resistant Pseudomonas aeruginosa (P. aeruginosa) strains have become a global threat due to their remarkable capability to survive and disseminate successfully by the acquisition of resistance genes. As a result, the treatment strategies have been severely compromised. Due to the insufficient available data regarding P. aeruginosa resistance from Pakistan, we aimed to investigate the resistance mechanisms of 249 P. aeruginosa strains by antimicrobial susceptibility testing, polymerase chain reaction for the detection of carbapenemases, aminoglycoside resistance genes, extended-spectrum beta-lactamases (ESBLs), sequence typing and plasmid typing. Furthermore, we tested silver nanoparticles (AgNPs) to evaluate their in vitro sensitivity against antimicrobial-resistant P. aeruginosa strains. We observed higher resistance against antimicrobials in the general surgery ward, general medicine ward and wound samples. Phenotypic carbapenemase-producer strains comprised 80.7% (201/249) with 89.0% (179/201) demonstrating genes encoding carbapenemases: blaNDM-1 (32.96%), blaOXA48 (37.43%), blaIMP (7.26%), blaVIM (5.03%), blaKPC-2 (1.12%), blaNDM-1/blaOXA48 (13.97%), blaOXA-48/blaVIM (1.68%) and blaVIM/blaIMP (0.56%). Aminoglycoside-modifying enzyme genes and 16S rRNA methylase variants were detected in 43.8% (109/249) strains: aac(6')-lb (12.8%), aac(3)-lla (12.0%), rmtB (21.1%), rmtC (11.0%), armA (12.8%), rmtD (4.6%), rmtF (6.4%), rmtB/aac(3)-lla (8.2%), rmtB/aac(6')-lla (7.3%) and rmtB/armA (3.6%). In total, 43.0% (77/179) of the strains coharbored carbapenemases and aminoglycoside resistance genes with 83.1% resistant to at least 1 agent in 3 or more classes and 16.9% resistant to every class of antimicrobials tested. Thirteen sequence types (STs) were identified: ST235, ST277, ST234, ST170, ST381, ST175, ST1455, ST1963, ST313, ST207, ST664, ST357 and ST348. Plasmid replicon types IncFI, IncFII, IncA/C, IncL/M, IncN, IncX, IncR and IncFIIK and MOB types F11, F12, H121, P131 and P3 were detected. Meropenem/AgNPs and Amikacin/AgNPs showed enhanced antibacterial activity. We reported the coexistence of carbapenemases and aminoglycoside resistance genes among carbapenem-resistant P. aeruginosa with diverse clonal lineages from Pakistan. Furthermore, we highlighted AgNP's potential role in handling future antimicrobial resistance concerns.
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Affiliation(s)
- Aamir Jamal Gondal
- Department of Biomedical Sciences, King Edward Medical University, Lahore 54000, Pakistan
| | - Nakhshab Choudhry
- Department of Biochemistry, King Edward Medical University, Lahore 54000, Pakistan
| | - Ammara Niaz
- Department of Biochemistry, King Edward Medical University, Lahore 54000, Pakistan
| | - Nighat Yasmin
- Department of Biomedical Sciences, King Edward Medical University, Lahore 54000, Pakistan
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Sastre-Femenia MÀ, Fernández-Muñoz A, Gomis-Font MA, Taltavull B, López-Causapé C, Arca-Suárez J, Martínez-Martínez L, Cantón R, Larrosa N, Oteo-Iglesias J, Zamorano L, Oliver A. Pseudomonas aeruginosa antibiotic susceptibility profiles, genomic epidemiology and resistance mechanisms: a nation-wide five-year time lapse analysis. THE LANCET REGIONAL HEALTH. EUROPE 2023; 34:100736. [PMID: 37753216 PMCID: PMC10518487 DOI: 10.1016/j.lanepe.2023.100736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 08/28/2023] [Accepted: 08/31/2023] [Indexed: 09/28/2023]
Abstract
Background Pseudomonas aeruginosa healthcare-associated infections are one of the top antimicrobial resistance threats world-wide. In order to analyze the current trends, we performed a Spanish nation-wide high-resolution analysis of the susceptibility profiles, the genomic epidemiology and the resistome of P. aeruginosa over a five-year time lapse. Methods A total of 3.180 nonduplicated P. aeruginosa clinical isolates from two Spanish nation-wide surveys performed in October 2017 and 2022 were analyzed. MICs of 13 antipseudomonals were determined by ISO-EUCAST. Multidrug resistance (MDR)/extensively drug resistance (XDR)/difficult to treat resistance (DTR)/pandrug resistance (PDR) profiles were defined following established criteria. All XDR/DTR isolates were subjected to whole genome sequencing (WGS). Findings A decrease in resistance to all tested antibiotics, including older and newer antimicrobials, was observed in 2022 vs 2017. Likewise, a major reduction of XDR (15.2% vs 5.9%) and DTR (4.2 vs 2.1%) profiles was evidenced, and even more patent among ICU isolates [XDR (26.0% vs 6.0%) and DTR (8.9% vs 2.6%)] (p < 0.001). The prevalence of Extended-spectrum β-lactamase/carbapenemase production was slightly lower in 2022 (2.1%. vs 3.1%, p = 0.064). However, there was a significant increase in the proportion of carbapenemase production among carbapenem-resistant strains (29.4% vs 18.1%, p = 0.0246). While ST175 was still the most frequent clone among XDR, a slight reduction in its prevalence was noted (35.9% vs 45.5%, p = 0.106) as opposed to ST235 which increased significantly (24.3% vs 12.3%, p = 0.0062). Interpretation While the generalized decrease in P. aeruginosa resistance, linked to a major reduction in the prevalence of XDR strains, is encouraging, the negative counterpart is the increase in the proportion of XDR strains producing carbapenemases, associated to the significant advance of the concerning world-wide disseminated hypervirulent high-risk clone ST235. Continued high-resolution surveillance, integrating phenotypic and genomic data, is necessary for understanding resistance trends and analyzing the impact of national plans on antimicrobial resistance. Funding MSD and the Instituto de Salud Carlos III, Ministerio de Ciencia e Innovación and Unión Europea-NextGenerationEU.
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Affiliation(s)
- Miquel Àngel Sastre-Femenia
- Servicio de Microbiología, Hospital Son Espases, Instituto de Investigación Sanitaria Illes Balears (IdISBa), CIBERINFEC, Palma de Mallorca, España
| | - Almudena Fernández-Muñoz
- Servicio de Microbiología, Hospital Son Espases, Instituto de Investigación Sanitaria Illes Balears (IdISBa), CIBERINFEC, Palma de Mallorca, España
| | - María Antonia Gomis-Font
- Servicio de Microbiología, Hospital Son Espases, Instituto de Investigación Sanitaria Illes Balears (IdISBa), CIBERINFEC, Palma de Mallorca, España
| | - Biel Taltavull
- Servicio de Microbiología, Hospital Son Espases, Instituto de Investigación Sanitaria Illes Balears (IdISBa), CIBERINFEC, Palma de Mallorca, España
| | - Carla López-Causapé
- Servicio de Microbiología, Hospital Son Espases, Instituto de Investigación Sanitaria Illes Balears (IdISBa), CIBERINFEC, Palma de Mallorca, España
| | - Jorge Arca-Suárez
- Servicio de Microbiología, Complexo Hospitalario Universitario A Coruña, Instituto Investigación Biomédica A Coruña (INIBIC), CIBERINFEC, A Coruña, España
| | - Luis Martínez-Martínez
- Unidad de Gestión Clínica de Microbiología, Hospital Universitario Reina Sofía, Departamento de Química Agrícola, Edafología y Microbiología, Universidad de Córdoba, Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), CIBERINFEC, Córdoba, España
| | - Rafael Cantón
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal- IRYCIS, CIBERINFEC, Madrid, España
| | - Nieves Larrosa
- Servicio de Microbiología, Hospital Universitario Vall d`Hebron, Vall d’Hebron Institut de Recerca (VHIR), Departamento de Genética y Microbiología, Universitat Autònoma de Barcelona, CIBERINFEC, Barcelona, España
| | - Jesús Oteo-Iglesias
- Centro Nacional de Microbiología, CIBERINFEC, Instituto de Salud Carlos III, Madrid, España
| | - Laura Zamorano
- Servicio de Microbiología, Hospital Son Espases, Instituto de Investigación Sanitaria Illes Balears (IdISBa), CIBERINFEC, Palma de Mallorca, España
| | - Antonio Oliver
- Servicio de Microbiología, Hospital Son Espases, Instituto de Investigación Sanitaria Illes Balears (IdISBa), CIBERINFEC, Palma de Mallorca, España
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Jordana-Lluch E, Barceló IM, Escobar-Salom M, Estévez MA, Zamorano L, Gómez-Zorrilla S, Sendra E, Oliver A, Juan C. The balance between antibiotic resistance and fitness/virulence in Pseudomonas aeruginosa: an update on basic knowledge and fundamental research. Front Microbiol 2023; 14:1270999. [PMID: 37840717 PMCID: PMC10569695 DOI: 10.3389/fmicb.2023.1270999] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 09/15/2023] [Indexed: 10/17/2023] Open
Abstract
The interplay between antibiotic resistance and bacterial fitness/virulence has attracted the interest of researchers for decades because of its therapeutic implications, since it is classically assumed that resistance usually entails certain biological costs. Reviews on this topic revise the published data from a general point of view, including studies based on clinical strains or in vitro-evolved mutants in which the resistance phenotype is seen as a final outcome, i.e., a combination of mechanisms. However, a review analyzing the resistance/fitness balance from the basic research perspective, compiling studies in which the different resistance pathways and respective biological costs are individually approached, was missing. Here we cover this gap, specifically focusing on Pseudomonas aeruginosa, a pathogen that stands out because of its extraordinary capacity for resistance development and for which a considerable number of recent and particular data on the interplay with fitness/virulence have been released. The revised information, split into horizontally-acquired vs. mutation-driven resistance, suggests a great complexity and even controversy in the resistance-fitness/virulence balance in the acute infection context, with results ranging from high costs linked to certain pathways to others that are seemingly cost-free or even cases of resistance mechanisms contributing to increased pathogenic capacities. The elusive mechanistic basis for some enigmatic data, knowledge gaps, and possibilities for therapeutic exploitation are discussed. The information gathered suggests that resistance-fitness/virulence interplay may be a source of potential antipseudomonal targets and thus, this review poses the elementary first step for the future development of these strategies harnessing certain resistance-associated biological burdens.
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Affiliation(s)
- Elena Jordana-Lluch
- Research Unit, University Hospital Son Espases-Health Research Institute of the Balearic Islands (IdISBa), Palma, Spain
- Department of Microbiology, University Hospital Son Espases, Palma, Spain
- Centro de Investigación Biomédica en Red, Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
| | - Isabel Mª Barceló
- Research Unit, University Hospital Son Espases-Health Research Institute of the Balearic Islands (IdISBa), Palma, Spain
- Department of Microbiology, University Hospital Son Espases, Palma, Spain
- Centro de Investigación Biomédica en Red, Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
| | - María Escobar-Salom
- Research Unit, University Hospital Son Espases-Health Research Institute of the Balearic Islands (IdISBa), Palma, Spain
- Department of Microbiology, University Hospital Son Espases, Palma, Spain
- Centro de Investigación Biomédica en Red, Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
| | - Miguel A. Estévez
- Research Unit, University Hospital Son Espases-Health Research Institute of the Balearic Islands (IdISBa), Palma, Spain
- Department of Microbiology, University Hospital Son Espases, Palma, Spain
| | - Laura Zamorano
- Research Unit, University Hospital Son Espases-Health Research Institute of the Balearic Islands (IdISBa), Palma, Spain
- Department of Microbiology, University Hospital Son Espases, Palma, Spain
- Centro de Investigación Biomédica en Red, Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
| | - Silvia Gómez-Zorrilla
- Centro de Investigación Biomédica en Red, Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
- Infectious Diseases Service, Hospital del Mar, Hospital del Mar Research Institute, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Universitat Autònoma de Barcelóna (UAB), Barcelona, Spain
| | - Elena Sendra
- Infectious Diseases Service, Hospital del Mar, Hospital del Mar Research Institute, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Universitat Autònoma de Barcelóna (UAB), Barcelona, Spain
| | - Antonio Oliver
- Research Unit, University Hospital Son Espases-Health Research Institute of the Balearic Islands (IdISBa), Palma, Spain
- Department of Microbiology, University Hospital Son Espases, Palma, Spain
- Centro de Investigación Biomédica en Red, Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
| | - Carlos Juan
- Research Unit, University Hospital Son Espases-Health Research Institute of the Balearic Islands (IdISBa), Palma, Spain
- Department of Microbiology, University Hospital Son Espases, Palma, Spain
- Centro de Investigación Biomédica en Red, Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
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Anbo M, Jelsbak L. A bittersweet fate: detection of serotype switching in Pseudomonas aeruginosa. Microb Genom 2023; 9:mgen000919. [PMID: 36748704 PMCID: PMC9973846 DOI: 10.1099/mgen.0.000919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
High-risk clone types in Pseudomonas aeruginosa are problematic global multidrug-resistant clones. However, apart from their ability to resist antimicrobial treatment, not much is known about what sets these clones apart from the multitude of other clones. In high-risk clone ST111, it has previously been shown that replacement of the native serotype biosynthetic gene cluster (O4) by a different gene cluster (O12) by horizontal gene transfer and recombination may have contributed to the global success of this clone. However, the extent to which isolates undergo this type of serotype switching has not been adequately explored in P. aeruginosa. In the present study, a bioinformatics tool has been developed and utilized to provide a first estimate of serotype switching in groups of multidrug resistant (MDR) clinical isolates. The tool detects serotype switching by analysis of core-genome phylogeny and in silico serotype. Analysis of a national survey of MDR isolates found a prevalence of 3.9 % of serotype-switched isolates in high-risk clone types ST111, ST244 and ST253. A global survey of MDR isolates was additionally analysed, and it was found that 2.3 % of isolates had undergone a serotype switch. To further understand this process, we determined the exact boundaries of the horizontally transferred serotype O12 island. We found that the size of the serotype island correlates with the clone type of the receiving isolate and additionally we found intra-clone type variations in size and boundaries. This suggests multiple serotype switch events. Moreover, we found that the housekeeping gene gyrA is co-transferred with the O12 serotype island, which prompted us to analyse this allele for all serotype O12 isolates. We found that 95 % of ST111 O12 isolates had a resistant gyrA allele and 86 % of all O12 isolates had a resistant gyrA allele. The rates of resistant gyrA alleles in isolates with other prevalent serotypes are all lower. Together, these results show that the transfer and acquisition of serotype O12 in high-risk clone ST111 has happened multiple times and may be facilitated by multiple donors, which clearly suggests a strong selection pressure for this process. However, gyrA-mediated antibiotic resistance may not be the only evolutionary driver.
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Affiliation(s)
- Mikkel Anbo
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kgs Lyngby, Denmark
| | - Lars Jelsbak
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kgs Lyngby, Denmark
- *Correspondence: Lars Jelsbak,
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5
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Hernández-Jiménez P, López-Medrano F, Fernández-Ruiz M, Silva JT, Corbella L, San-Juan R, Lizasoain M, Díaz-Regañón J, Viedma E, Aguado JM. Risk Factors and Outcomes for Multidrug Resistant Pseudomonas aeruginosa Infection in Immunocompromised Patients. Antibiotics (Basel) 2022; 11:antibiotics11111459. [PMID: 36358114 PMCID: PMC9686626 DOI: 10.3390/antibiotics11111459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/17/2022] [Accepted: 10/20/2022] [Indexed: 11/29/2022] Open
Abstract
Background: Pseudomonas aeruginosa (PSA) infection often occurs in immunocompromised patients, which also face an increased risk of multidrug-resistant (MDR) bacteria. A deeper knowledge of the risk factors for MDR-PSA infection in this patient population may help to choose appropriate empirical antibiotic therapy. Methods: a single-center case-control (1:2) retrospective study that included 48 patients with underlying immunosuppression developing MDR-PSA infection (cases) and 96 patients also immunocompromised that were infected with non-MDR-PSA (controls) was conducted. Both groups were matched by site of infection, clinical features and type of immunosuppression. Risk factors for MDR-PSA were assessed by logistic regression. Clinical outcomes were also compared between both groups. Results: immunosuppression was due to solid cancer in 63 (43.8%) patients, solid organ transplantation in 39 (27.1%), hematological disease in 35 (24.3%) and other causes in 7 (4.9%). Independent risk factors for MDR-PSA infection were diabetes mellitus (odds ratio [OR]: 4.74; 95% confidence interval [CI]: 1.63−13.79; p = 0.004), antibiotic therapy in the previous 3 months (OR: 5.32; 95% CI: 1.93−14.73; p = 0.001), previous MDR-PSA colonization (OR: 42.1; 95% CI: 4.49−394.8; p = 0.001) and septic shock (OR: 3.73; 95% CI: 1.36−10.21; p = 0.010). MDR-PSA cases were less likely to receive adequate empirical therapy (14 [29.2%] vs. 69 [71.9%]; p < 0.001). 30-day clinical improvement was less common in MDR-PSA cases (25 [52.1%] vs. 76 [79.2%]; p = 0.001). Conclusions: diabetes mellitus, previous MDR-PSA colonization, prior receipt of antibiotics and septic shock acted as risk factors for developing MDR-PSA infections in immunocompromised patients, who have a poorer outcome than those infected with non-MDR-PSA strains.
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Affiliation(s)
- Pilar Hernández-Jiménez
- Unit of Infectious Diseases, Hospital Universitario “12 de Octubre”, Instituto de Investigación Sanitaria Hospital “12 de Octubre” (imas12), 28041 Madrid, Spain
- Department of Medicine, School of Medicine, Universidad Complutense, 28040 Madrid, Spain
- Correspondence: ; Tel.: +34-659537429
| | - Francisco López-Medrano
- Unit of Infectious Diseases, Hospital Universitario “12 de Octubre”, Instituto de Investigación Sanitaria Hospital “12 de Octubre” (imas12), 28041 Madrid, Spain
- Department of Medicine, School of Medicine, Universidad Complutense, 28040 Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid 28029, Spain
| | - Mario Fernández-Ruiz
- Unit of Infectious Diseases, Hospital Universitario “12 de Octubre”, Instituto de Investigación Sanitaria Hospital “12 de Octubre” (imas12), 28041 Madrid, Spain
- Department of Medicine, School of Medicine, Universidad Complutense, 28040 Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid 28029, Spain
| | - J. Tiago Silva
- Unit of Infectious Diseases, Hospital Universitario “12 de Octubre”, Instituto de Investigación Sanitaria Hospital “12 de Octubre” (imas12), 28041 Madrid, Spain
- Department of Medicine, School of Medicine, Universidad Complutense, 28040 Madrid, Spain
| | - Laura Corbella
- Unit of Infectious Diseases, Hospital Universitario “12 de Octubre”, Instituto de Investigación Sanitaria Hospital “12 de Octubre” (imas12), 28041 Madrid, Spain
- Department of Medicine, School of Medicine, Universidad Complutense, 28040 Madrid, Spain
| | - Rafael San-Juan
- Unit of Infectious Diseases, Hospital Universitario “12 de Octubre”, Instituto de Investigación Sanitaria Hospital “12 de Octubre” (imas12), 28041 Madrid, Spain
- Department of Medicine, School of Medicine, Universidad Complutense, 28040 Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid 28029, Spain
| | - Manuel Lizasoain
- Unit of Infectious Diseases, Hospital Universitario “12 de Octubre”, Instituto de Investigación Sanitaria Hospital “12 de Octubre” (imas12), 28041 Madrid, Spain
- Department of Medicine, School of Medicine, Universidad Complutense, 28040 Madrid, Spain
| | | | - Esther Viedma
- Department of Microbiology, Hospital Universitario “12 de Octubre”, Instituto de Investigación Sanitaria Hospital “12 de Octubre” (imas12), 28041 Madrid, Spain
| | - José María Aguado
- Unit of Infectious Diseases, Hospital Universitario “12 de Octubre”, Instituto de Investigación Sanitaria Hospital “12 de Octubre” (imas12), 28041 Madrid, Spain
- Department of Medicine, School of Medicine, Universidad Complutense, 28040 Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid 28029, Spain
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Emergence and Transfer of Plasmid-Harbored rmtB in a Clinical Multidrug-Resistant Pseudomonas aeruginosa Strain. Microorganisms 2022; 10:microorganisms10091818. [PMID: 36144421 PMCID: PMC9500886 DOI: 10.3390/microorganisms10091818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/03/2022] [Accepted: 09/08/2022] [Indexed: 11/17/2022] Open
Abstract
Multidrug-resistant (MDR) Pseudomonas aeruginosa poses a great challenge to clinical treatment. In this study, we characterized a ST768 MDR P. aeruginosa strain, Pa150, that was isolated from a diabetic foot patient. The minimum inhibitory concentration (MIC) assay showed that Pa150 was resistant to almost all kinds of antibiotics, especially aminoglycosides. Whole genome sequencing revealed multiple antibiotic resistant genes on the chromosome and a 437-Kb plasmid (named pTJPa150) that harbors conjugation-related genes. A conjugation assay verified its self-transmissibility. On the pTJPa150 plasmid, we identified a 16S rRNA methylase gene, rmtB, that is flanked by mobile genetic elements (MGEs). The transfer of the pTJPa150 plasmid or the cloning of the rmtB gene into the reference strain, PAO1, significantly increased the bacterial resistance to aminoglycoside antibiotics. To the best of our knowledge, this is the first report of an rmtB-carrying conjugative plasmid isolated from P. aeruginosa, revealing a novel possible transmission mechanism of the rmtB gene.
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Fonseca ÉL, Morgado SM, Caldart RV, Freitas F, Vicente ACP. Emergence of a VIM-2-producing XDR Pseudomonas aeruginosa ST309 in South America: a comparative genomic analysis. Int J Antimicrob Agents 2021; 59:106507. [PMID: 34958864 DOI: 10.1016/j.ijantimicag.2021.106507] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 12/14/2021] [Accepted: 12/18/2021] [Indexed: 11/18/2022]
Abstract
Pseudomonas aeruginosa has been considered a top priority pathogen associated with elevated morbidity and mortality. Worldwide outbreaks have been associated with few high-risk epidemic P. aeruginosa lineages. However, the biological features involved with the persistence and spread of such lineages among clinical settings remain to be unraveled. This study reports the emergence of an XDR ST309 P. aeruginosa in South America/Brazil, more precisely, in the Amazon region. Genomic analyses were performed with 42 complete and draft ST309 genomes, giving insights into its epidemiology, resistome, and mobilome. Heterogeneous distribution of acquired antimicrobial resistance genes among ST309 genomes was observed, which included blaVIM-2, blaIMP-15, and qnrVC1, all of them associated with class 1 integrons. The mobilome mining showed the presence of Integrative and Conjugative Elements, transposons, and genomic islands harbouring a huge arsenal of heavy metal resistance determinants, which probably provided adaptive advantages to ST309 lineage.
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Affiliation(s)
- Érica L Fonseca
- Laboratório de Genética Molecular de Microrganismos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (FIOCRUZ), Avenida Brasil 4365, Manguinhos, Rio de Janeiro, RJ, 21040-900, Brazil.
| | - Sérgio M Morgado
- Laboratório de Genética Molecular de Microrganismos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (FIOCRUZ), Avenida Brasil 4365, Manguinhos, Rio de Janeiro, RJ, 21040-900, Brazil
| | | | - Fernanda Freitas
- Laboratório de Genética Molecular de Microrganismos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (FIOCRUZ), Avenida Brasil 4365, Manguinhos, Rio de Janeiro, RJ, 21040-900, Brazil
| | - Ana Carolina P Vicente
- Laboratório de Genética Molecular de Microrganismos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (FIOCRUZ), Avenida Brasil 4365, Manguinhos, Rio de Janeiro, RJ, 21040-900, Brazil
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Laborda P, Sanz-García F, Hernando-Amado S, Martínez JL. Pseudomonas aeruginosa: an antibiotic resilient pathogen with environmental origin. Curr Opin Microbiol 2021; 64:125-132. [PMID: 34710741 DOI: 10.1016/j.mib.2021.09.010] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 08/31/2021] [Accepted: 09/23/2021] [Indexed: 12/24/2022]
Abstract
Pseudomonas aeruginosa, a bacterium characterized for its low antibiotics' susceptibility, is one of the most relevant opportunistic pathogens, causing infections at hospitals and in cystic fibrosis patients. Besides its relevance for human health, P. aeruginosa colonizes environmental ecosystems; therefore the elements driving its infectivity and antibiotic resistance must be analyzed from a One-Health perspective. Although some epidemic clones have been described, there are not specific lineages linked to infections, suggesting that P. aeruginosa virulence and antibiotic resistance determinants evolved in nature to play functions other than infecting the human host and avoiding antimicrobial treatment. Herein, we review current information on the population structure of P. aeruginosa and on the functional role that its resistance and virulence determinants have in non-clinical ecosystems.
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Affiliation(s)
- Pablo Laborda
- Centro Nacional de Biotecnología, CSIC, 28049, Madrid, Spain
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9
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Recio R, Viedma E, González-Bodí S, Villa J, Orellana MÁ, Mancheño-Losa M, Lora-Tamayo J, Chaves F. Clinical and bacterial characteristics of Pseudomonas aeruginosa affecting the outcome of patients with bacteraemic pneumonia. Int J Antimicrob Agents 2021; 58:106450. [PMID: 34644604 DOI: 10.1016/j.ijantimicag.2021.106450] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 09/22/2021] [Accepted: 10/02/2021] [Indexed: 12/29/2022]
Abstract
Few studies have assessed the clinical and bacterial characteristics of Pseudomonas aeruginosa (PA) bacteraemic pneumonia (BP) episodes. This study analysed all non-duplicate PA-BP episodes from a tertiary hospital in 2013-2017. Epidemiology, clinical data, antimicrobial therapy and outcomes were recorded. Whole-genome sequencing was performed on PA blood isolates. The impact on early and late overall mortality of host, antimicrobial treatment and pathogen factors was assessed by multivariate logistic regression analysis. Of 55 PA-BP episodes, 32 (58.2%) were caused by extensively drug-resistant (XDR) PA. ST175 (32.7%) and ST235 (25.5%) were the most frequent high-risk clones. β-Lactamases/carbapenemases were detected in 29 isolates, including blaVIM-2 (27.2%) and blaGES type (25.5%) [blaGES-5 (20.0%), blaGES-1 (3.6%) and blaGES-20 (1.8%)]. The most prevalent O-antigen serotypes were O4 (34.5%) and O11 (30.9%). Overall, an extensive virulome was identified in all isolates. Early mortality (56.4%) was independently associated with severe neutropenia (aOR = 4.64, 95% CI 1.11-19.33; P = 0.035) and inappropriate empirical antimicrobial therapy (aOR = 5.71, 95% CI 1.41-22.98; P = 0.014). Additionally, late mortality (67.3%) was influenced by septic shock (aOR = 8.85, 95% CI 2.00-39.16; P = 0.004) and XDR phenotype (aOR = 5.46, 95% CI 1.25-23.85; P = 0.024). Moreover, specific genetic backgrounds [ST235, blaGES, gyrA (T83I), parC (S87L), exoU and O11 serotype] showed significant differences in patient outcomes. Our results confirm the high mortality associated with PA-BP. Besides relevant clinical characteristics and inappropriate empirical therapy, bacteria-specific genetics factors, such as XDR phenotype, adversely affect the outcome of PA-BP.
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Affiliation(s)
- Raúl Recio
- Department of Clinical Microbiology, Instituto de Investigación Hospital 12 de Octubre (imas12), Hospital Universitario 12 de Octubre, Madrid, Spain.
| | - Esther Viedma
- Department of Clinical Microbiology, Instituto de Investigación Hospital 12 de Octubre (imas12), Hospital Universitario 12 de Octubre, Madrid, Spain
| | - Sara González-Bodí
- Department of Clinical Microbiology, Instituto de Investigación Hospital 12 de Octubre (imas12), Hospital Universitario 12 de Octubre, Madrid, Spain
| | - Jennifer Villa
- Department of Clinical Microbiology, Instituto de Investigación Hospital 12 de Octubre (imas12), Hospital Universitario 12 de Octubre, Madrid, Spain
| | - María Ángeles Orellana
- Department of Clinical Microbiology, Instituto de Investigación Hospital 12 de Octubre (imas12), Hospital Universitario 12 de Octubre, Madrid, Spain
| | - Mikel Mancheño-Losa
- Department of Internal Medicine, Instituto de Investigación Hospital 12 de Octubre (imas12), Hospital Universitario 12 de Octubre, Madrid, Spain
| | - Jaime Lora-Tamayo
- Department of Internal Medicine, Instituto de Investigación Hospital 12 de Octubre (imas12), Hospital Universitario 12 de Octubre, Madrid, Spain
| | - Fernando Chaves
- Department of Clinical Microbiology, Instituto de Investigación Hospital 12 de Octubre (imas12), Hospital Universitario 12 de Octubre, Madrid, Spain
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Gupte A, Jyot J, Ravi M, Ramphal R. High pyocyanin production and non-motility of Pseudomonas aeruginosa isolates are correlated with septic shock or death in bacteremic patients. PLoS One 2021; 16:e0253259. [PMID: 34115807 PMCID: PMC8195364 DOI: 10.1371/journal.pone.0253259] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 06/01/2021] [Indexed: 12/26/2022] Open
Abstract
Studies of the outcome of Pseudomonas aeruginosa bacteremia (Pab) have focused mainly on antibiotic appropriateness. However, P. aeruginosa possesses many virulence factors whose roles in outcomes have not been examined in humans, except for the type III secretion system (T3SS) toxins. The purpose of this study was to examine the role of virulence factors other than the T3SS toxins. Bacterial isolates were collected from 75 patients who suffered from Pa blood stream infections. Host factors such as neutropenia, immunosuppression, comorbidities, time to effective antibiotics, source of bacteremia, and presence of multidrug resistant (MDR) isolate were studied. The isolates were analyzed for the presence of toxin genes, proteolytic activity, swimming and twitching motility, and pyocyanin production. The data were analyzed to ascertain which virulence factors correlated with poor outcomes defined as septic shock or death (SS) within 7 days. Septic shock or death occurred in 25/75 patients. Univariate analysis identified age as a host factor that exerted a significant effect on these outcomes. Ineffective antibiotics administered during the first 24 hours of treatment or MDR P. aeruginosa did not influence the frequency of SS, nor did the presence of lasB, exoA, exoS exoU, plcH genes and proteolytic activity. However, 6/8 patients infected with non-motile isolates, developed SS, p = 0.014 and 5/6 isolates that produced large amounts of pyocyanin (>18ug/ml), were associated with SS, p = 0.014. Multivariate analysis indicated that the odds ratio (OR) for development of SS with a non-motile isolate was 6.8, with a 95% confidence interval (CI) (1.37, 51.5), p = 0.030 and with high pyocyanin producing isolates, an OR of 16.9, 95% CI = (2.27, 360), p = .017. This study evaluating the role of microbial factors that significantly effect outcomes following Pa bloodstream infection suggests that P. aeruginosa strains showing high pyocyanin production and the lack of motility independently increase the risk of SS.
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Affiliation(s)
- Asmita Gupte
- Division of Infectious Diseases and Global Medicine, Department of Medicine, University of Florida, Gainesville, Florida, United States of America
- * E-mail: (AG); (RR)
| | - Jeevan Jyot
- Division of Infectious Diseases and Global Medicine, Department of Medicine, University of Florida, Gainesville, Florida, United States of America
- Department of Pharmaceutical Outcomes & Policy, College of Pharmacy, University of Florida, Gainesville, Florida, United States of America
| | - Malleswari Ravi
- Division of Infectious Diseases and Global Medicine, Department of Medicine, University of Florida, Gainesville, Florida, United States of America
| | - Reuben Ramphal
- Division of Infectious Diseases and Global Medicine, Department of Medicine, University of Florida, Gainesville, Florida, United States of America
- * E-mail: (AG); (RR)
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11
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Saleem H, Mazhar S, Syed Q, Javed MQ, Adnan A. Bio-characterization of food grade pyocyanin bio-pigment extracted from chromogenic Pseudomonas species found in Pakistani native flora. ARAB J CHEM 2021. [DOI: 10.1016/j.arabjc.2021.103005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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12
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Phenotypic and Genomic Comparison of the Two Most Common ExoU-Positive Pseudomonas aeruginosa Clones, PA14 and ST235. mSystems 2020; 5:5/6/e01007-20. [PMID: 33293405 PMCID: PMC7743143 DOI: 10.1128/msystems.01007-20] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Genotyping of 2,882 Pseudomonas aeruginosa isolates that had been collected during the last 40 years identified the ExoU-positive lineages PA14 (ST253) and ST235 as the second and third most frequent clones in the P. aeruginosa population. Both clones were approximately 2-fold more frequently detected in animate habitats than in soil or aquatic habitats. While ST253 clone isolates were causing mainly acute and chronic infections in humans, ST235 isolates had been preferentially collected from hospitalized patients with severe acute infections, particularly, keratitis, urinary tract infections, burn wounds, and ventilator-associated pneumonia. The two major exoU clones differed substantially in the composition and flexibility of the accessory genome and by more than 8,000 amino acid sequences. Pronounced sequence variation between orthologs was noted in genes encoding elements of secretion systems and secreted effector molecules, including the type III secretion system, indicating the modes of action of the different clones. When comparing representatives of the two clones in batch culture, the PA14 strain orchestrated the quorum sensing circuitry for the expression of pathogenic traits and stopped growing in batch culture when it entered the stationary phase, but the quorum sensing-deficient ST235 strain expressed high type III secretion activity and continued to grow and to divide. In summary, unrestricted growth, high constitutive type III secretion activity, and facilitated uptake of foreign DNA could be major features that have made ST235 a global high-risk clone associated with poor outcomes of acute nosocomial infections.IMPORTANCE The ubiquitous and metabolically versatile environmental bacterium Pseudomonas aeruginosa can cause infections in a wide variety of hosts, including insects, plants, animals, and humans. P. aeruginosa is one of the ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) pathogens that are the major cause of nosocomial infections in the United States and are a threat all over the world because of their capacity to become increasingly resistant to all available antibiotics. Most experimental work on P. aeruginosa has been performed with reference strains PAO1 and PA14, providing deep insight into key metabolic and regulatory pathways thought to be applicable to all P. aeruginosa strains. However, this comparative study on the two most common exoU-positive clones taught us that there are major lineages in the population such as the global high-risk clone ST235 that exhibit uncommon traits of lifestyle, genome mobility, and pathogenicity distinct from those in our knowledge gained from the studies with the reference strains.
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Rodrigues YC, Furlaneto IP, Maciel AHP, Quaresma AJPG, de Matos ECO, Conceição ML, Vieira MCDS, Brabo GLDC, Sarges EDSNF, Lima LNGC, Lima KVB. High prevalence of atypical virulotype and genetically diverse background among Pseudomonas aeruginosa isolates from a referral hospital in the Brazilian Amazon. PLoS One 2020; 15:e0238741. [PMID: 32911510 PMCID: PMC7482967 DOI: 10.1371/journal.pone.0238741] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Accepted: 08/21/2020] [Indexed: 12/23/2022] Open
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen causing different types of infections, particularly in intensive care unit patients. Characteristics that favor its persistence artificial environments are related to its high adaptability, wide arsenal of virulence factors and resistance to several antimicrobial classes. Among the several virulence determinants, T3SS stands as the most important due to the clinical impact of exoS and exoU genes in patient’s outcome. The molecular characterization of P. aeruginosa isolates helps in the comprehension of transmission dynamics and enhance knowledge of virulence and resistance roles in infection process. In the present study, we investigated virulence and resistance properties and the genetic background of P. aeruginosa isolated from ICUs patients at a referral hospital in Brazilian Amazon. A total of 54 P. aeruginosa isolates were characterized by detecting 19 virulence-related genes, antimicrobial susceptibility testing, molecular detection of β-lactamase-encoding genes and genotyping by MLST and rep-PCR. Our findings showed high prevalence of virulence-related markers, where 53.7% of the isolates presented at least 17 genes among the 19 investigated (P = 0.01). The rare exoS+/exoU+ cytotoxic virulotype was detected in 55.6% of isolates. Antimicrobial susceptibility testing revealed percentages of antibiotic resistance above 50% to carbapenems, cephalosporins and fluoroquinolones associated to MDR/XDR isolates. Isolates harboring both blaSPM-1 and blaOXA genes were also detected. Genotyping methods demonstrated a wide genetic diversity of strains spread among the different intensive care units, circulation of international MDR/XDR high-risk clones (ST111, ST235, ST244 and ST277) and emergence of seven novel MLST lineages. Finally, our findings highlight the circulation of strains with high virulence potential and resistance to antimicrobials and may be useful on comprehension of pathogenicity process, treatment guidance and establishment of strategies to control the spread of epidemic P. aeruginosa strains.
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Affiliation(s)
- Yan Corrêa Rodrigues
- Programa de Pós-graduação em Biologia Parasitária na Amazônia, Centro de Ciências Biológicas e da Saúde, Universidade do Estado do Pará (UEPA), Belém, Pará, Brazil
- * E-mail: (YCR); (KVBL)
| | - Ismari Perini Furlaneto
- Programa de Pós-graduação em Educação em Saúde, Centro Universitário do Pará (CESUPA), Belém, Pará Brazil
| | - Arthur Henrique Pinto Maciel
- Laboratório de Biologia Molecular, Seção de Bacteriologia e Micologia, Instituto Evandro Chagas (IEC), Ministério da Saúde, Ananindeua, Pará, Brazil
| | - Ana Judith Pires Garcia Quaresma
- Laboratório de Biologia Molecular, Seção de Bacteriologia e Micologia, Instituto Evandro Chagas (IEC), Ministério da Saúde, Ananindeua, Pará, Brazil
| | - Eliseth Costa Oliveira de Matos
- Departamento de Patologia, Centro de Ciências Biológicas e da Saúde, Universidade do Estado do Pará (UEPA), Belém, Pará, Brazil
| | - Marília Lima Conceição
- Programa de Pós-graduação em Biologia Parasitária na Amazônia, Centro de Ciências Biológicas e da Saúde, Universidade do Estado do Pará (UEPA), Belém, Pará, Brazil
| | - Marcelo Cleyton da Silva Vieira
- Laboratório de Biologia Molecular, Seção de Bacteriologia e Micologia, Instituto Evandro Chagas (IEC), Ministério da Saúde, Ananindeua, Pará, Brazil
| | - Giulia Leão da Cunha Brabo
- Laboratório de Biologia Molecular, Seção de Bacteriologia e Micologia, Instituto Evandro Chagas (IEC), Ministério da Saúde, Ananindeua, Pará, Brazil
| | | | - Luana Nepomuceno Godim Costa Lima
- Programa de Pós-graduação em Biologia Parasitária na Amazônia, Centro de Ciências Biológicas e da Saúde, Universidade do Estado do Pará (UEPA), Belém, Pará, Brazil
- Laboratório de Biologia Molecular, Seção de Bacteriologia e Micologia, Instituto Evandro Chagas (IEC), Ministério da Saúde, Ananindeua, Pará, Brazil
| | - Karla Valéria Batista Lima
- Programa de Pós-graduação em Biologia Parasitária na Amazônia, Centro de Ciências Biológicas e da Saúde, Universidade do Estado do Pará (UEPA), Belém, Pará, Brazil
- Laboratório de Biologia Molecular, Seção de Bacteriologia e Micologia, Instituto Evandro Chagas (IEC), Ministério da Saúde, Ananindeua, Pará, Brazil
- * E-mail: (YCR); (KVBL)
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Loconsole D, Accogli M, Monaco M, Del Grosso M, De Robertis AL, Morea A, Capozzi L, Del Sambro L, Simone A, De Letteriis V, Quarto M, Parisi A, Chironna M. First detection of autochthonous extensively drug-resistant NDM-1 Pseudomonas aeruginosa ST235 from a patient with bloodstream infection in Italy, October 2019. Antimicrob Resist Infect Control 2020; 9:73. [PMID: 32450907 PMCID: PMC7249406 DOI: 10.1186/s13756-020-00734-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 05/09/2020] [Indexed: 12/15/2022] Open
Abstract
Background Pseudomonas aeruginosa (PA) is one of the most common and serious causes of healthcare-associated bacteremia. The emergence and dissemination of multidrug-resistant (MDR) and extensively drug-resistant (XDR) PA strains pose a major clinical concern. ST235-PA is a high-risk clone which shows a high capacity to acquire antibiotic resistance. Here we describe the first autochthonous New Delhi metallo-β-lactamase (NDM)-producing Pseudomonas aeruginosa ST235 identified in Italy. Case presentation In October 2019, a patient residing in an elderly health care and rehabilitation facility, was hospitalized and died from sepsis caused by an XDR-PA. The strain belonged to the high-risk clone sequence type ST235. Whole genome sequencing (WGS) revealed the presence of genes encoding NDM-1 and multiple β-lactamases, many clinically significant multidrug efflux pump complexes and also the virulence gene ExoU, which is associated with a high cytotoxic phenotype. Conclusions Few strains of NDM-1-PA have been identified worldwide, all belonging to ST235. The combination of ST235 and ExoU is a predictor of highly unfavorable prognosis. The potential spread of these high-risk clones in healthcare settings is worrisome because treatment options are limited. Early identification of high-risk clones could help in outbreaks investigation and infections control.
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Affiliation(s)
- Daniela Loconsole
- Department of Biomedical Sciences and Human Oncology, Hygiene Unit, University of Bari "Aldo Moro", P.zza G. Cesare 11, 70124, Bari, Italy
| | - Marisa Accogli
- Department of Biomedical Sciences and Human Oncology, Hygiene Unit, University of Bari "Aldo Moro", P.zza G. Cesare 11, 70124, Bari, Italy
| | - Monica Monaco
- Department of Infectious Diseases, Istituto Superiore di Sanità, Roma, Italy
| | - Maria Del Grosso
- Department of Infectious Diseases, Istituto Superiore di Sanità, Roma, Italy
| | - Anna Lisa De Robertis
- Department of Biomedical Sciences and Human Oncology, Hygiene Unit, University of Bari "Aldo Moro", P.zza G. Cesare 11, 70124, Bari, Italy
| | - Anna Morea
- Department of Biomedical Sciences and Human Oncology, Hygiene Unit, University of Bari "Aldo Moro", P.zza G. Cesare 11, 70124, Bari, Italy
| | - Loredana Capozzi
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Foggia, Italy
| | - Laura Del Sambro
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Foggia, Italy
| | | | | | - Michele Quarto
- Department of Biomedical Sciences and Human Oncology, Hygiene Unit, University of Bari "Aldo Moro", P.zza G. Cesare 11, 70124, Bari, Italy
| | - Antonio Parisi
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Foggia, Italy
| | - Maria Chironna
- Department of Biomedical Sciences and Human Oncology, Hygiene Unit, University of Bari "Aldo Moro", P.zza G. Cesare 11, 70124, Bari, Italy.
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