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Mó I, da Silva GJ. Tackling Carbapenem Resistance and the Imperative for One Health Strategies-Insights from the Portuguese Perspective. Antibiotics (Basel) 2024; 13:557. [PMID: 38927223 PMCID: PMC11201282 DOI: 10.3390/antibiotics13060557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2024] [Revised: 06/09/2024] [Accepted: 06/11/2024] [Indexed: 06/28/2024] Open
Abstract
Carbapenemases, a class of enzymes specialized in the hydrolysis of carbapenems, represent a significant threat to global public health. These enzymes are classified into different Ambler's classes based on their active sites, categorized into classes A, D, and B. Among the most prevalent types are IMI/NMC-A, KPC, VIM, IMP, and OXA-48, commonly associated with pathogenic species such as Acinetobacter baumannii, Klebsiella pneumoniae, and Pseudomonas aeruginosa. The emergence and dissemination of carbapenemase-producing bacteria have raised substantial concerns due to their ability to infect humans and animals (both companion and food-producing) and their presence in environmental reservoirs. Adopting a holistic One Health approach, concerted efforts have been directed toward devising comprehensive strategies to mitigate the impact of antimicrobial resistance dissemination. This entails collaborative interventions, highlighting proactive measures by global organizations like the World Health Organization, the Center for Disease Control and Prevention, and the Food and Agriculture Organization. By synthesizing the evolving landscape of carbapenemase epidemiology in Portugal and tracing the trajectory from initial isolated cases to contemporary reports, this review highlights key factors driving antibiotic resistance, such as antimicrobial use and healthcare practices, and underscores the imperative for sustained vigilance, interdisciplinary collaboration, and innovative interventions to curb the escalating threat posed by antibiotic-resistant pathogens. Finally, it discusses potential alternatives and innovations aimed at tackling carbapenemase-mediated antibiotic resistance, including new therapies, enhanced surveillance, and public awareness campaigns.
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Affiliation(s)
- Inês Mó
- Faculty of Pharmacy, University of Coimbra, 3000-548 Coimbra, Portugal;
| | - Gabriela Jorge da Silva
- Faculty of Pharmacy, University of Coimbra, 3000-548 Coimbra, Portugal;
- CNC, Center for Neuroscience and Cell Biology, 3004-504 Coimbra, Portugal
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Faria NA, Touret T, Simões AS, Palos C, Bispo S, Cristino JM, Ramirez M, Carriço J, Pinto M, Toscano C, Gonçalves E, Gonçalves ML, Costa A, Araújo M, Duarte A, de Lencastre H, Serrano M, Sá-Leão R, Miragaia M. Genomic insights into the expansion of carbapenem-resistant Klebsiella pneumoniae within Portuguese hospitals. J Hosp Infect 2024; 148:62-76. [PMID: 38554808 DOI: 10.1016/j.jhin.2024.02.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 01/31/2024] [Accepted: 02/19/2024] [Indexed: 04/02/2024]
Abstract
Carbapenem-resistant Klebsiella pneumoniae (CR-KP) are a public health concern, causing infections with a high mortality rate, limited therapeutic options and challenging infection control strategies. In Portugal, the CR-KP rate has increased sharply, but the factors associated with this increase are poorly explored. In order to address this question, phylogenetic and resistome analysis were used to compare the draft genomes of 200 CR-KP isolates collected in 2017-2019 from five hospitals in the Lisbon region, Portugal. Most CR-KP belonged to sequence type (ST) 13 (29%), ST17 (15%), ST348 (13%), ST231 (12%) and ST147 (7%). Carbapenem resistance was conferred mostly by the presence of KPC-3 (74%) or OXA-181 (18%), which were associated with IncF/IncN and IncX plasmids, respectively. Almost all isolates were multi-drug resistant, harbouring resistance determinants to aminoglycosides, beta-lactams, trimethoprim, fosfomycin, quinolones and sulphonamides. In addition, 11% of isolates were resistant to colistin. Colonizing and infecting isolates were highly related, and most colonized patients (89%) reported a previous hospitalization. Moreover, among the 171 events of cross-dissemination identified by core genome multi-locus sequence typing data analysis (fewer than five allelic differences), 41 occurred between different hospitals and 130 occurred within the same hospital. The results suggest that CR-KP dissemination in the Lisbon region results from acquisition of carbapenemases in mobile genetic elements, influx of CR-KP into the hospitals by colonized ambulatory patients, and transmission of CR-KP within and between hospitals. Prudent use of carbapenems, patient screening at hospital entry, and improvement of infection control are needed to decrease the burden of CR-KP infection in Portugal.
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Affiliation(s)
- N A Faria
- Laboratory of Bacterial Evolution and Molecular Epidemiology, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Lisbon, Portugal; Laboratory of Molecular Genetics, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Lisbon, Portugal
| | - T Touret
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Lisbon, Portugal
| | - A S Simões
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Lisbon, Portugal
| | - C Palos
- Hospital Beatriz Ângelo, Lisbon, Portugal
| | - S Bispo
- Hospital Beatriz Ângelo, Lisbon, Portugal
| | - J M Cristino
- Centro Hospitalar Lisboa Norte, Lisbon, Portugal
| | - M Ramirez
- Centro Hospitalar Lisboa Norte, Lisbon, Portugal; Instituto de Microbiologia, Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - J Carriço
- Centro Hospitalar Lisboa Norte, Lisbon, Portugal; Instituto de Microbiologia, Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - M Pinto
- Centro Hospitalar Lisboa Central, Lisbon, Portugal
| | - C Toscano
- Centro Hospitalar Lisboa Ocidental, Lisbon, Portugal
| | - E Gonçalves
- Centro Hospitalar Lisboa Ocidental, Lisbon, Portugal
| | | | - A Costa
- Hospital dos SAMS, Lisbon, Portugal
| | - M Araújo
- Laboratory of Bacterial Evolution and Molecular Epidemiology, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Lisbon, Portugal
| | - A Duarte
- Faculdade de Farmácia, Universidade de Lisboa, Lisbon, Portugal; Centro de investigação Interdisciplinar Egas Moniz, Instituto Universitário Egas Moniz, Almada, Portugal
| | - H de Lencastre
- Laboratory of Molecular Genetics, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Lisbon, Portugal; Laboratory of Microbiology and Infectious Diseases, The Rockefeller University, New York, USA
| | - M Serrano
- Laboratory of Microbial Development, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Lisbon, Portugal
| | - R Sá-Leão
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Lisbon, Portugal
| | - M Miragaia
- Laboratory of Bacterial Evolution and Molecular Epidemiology, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Lisbon, Portugal.
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3
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Moreira da Silva J, Menezes J, Fernandes L, Santos Costa S, Amaral A, Pomba C. Carbapenemase-producing Enterobacterales strains causing infections in companion animals-Portugal. Microbiol Spectr 2024; 12:e0341623. [PMID: 38446073 PMCID: PMC10986603 DOI: 10.1128/spectrum.03416-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 02/15/2024] [Indexed: 03/07/2024] Open
Abstract
An increase in Klebsiella pneumoniae carbapenem-resistant human nosocomial strains is occurring in Europe, namely with the blaOXA-48-like and blaKPC-like genes. We determined the prevalence of carbapenemase-producing Enterobacterales clinical strains in companion animals in Portugal and characterized their mobile genetic elements. Susceptibility data of a consecutive collection of 977 Enterobacterales clinical strains from a Portuguese private veterinary diagnostic laboratory were evaluated (January-December 2020). Additional phenotypical and genotypical assays were performed in a subset of 261 strains with a resistant phenotype. Whole-genome sequencing was performed for carbapenemase-producing strains. The frequency of carbapenemase-producing Enterobacterales clinical strains in companion animals in Portugal was 0.51% (n = 5/977). Thus, five strains were characterized: (i) one OXA-181-producing K. pneumoniae ST273, (ii) two KPC-3-producing K. pneumoniae ST147; (iii) one KPC-3-producing K. pneumoniae ST392; and (iv) one OXA-48-producing E. coli ST127. The blaKPC-3 gene was located on transposon Tn4401d on IncFIA type plasmid for the K. pneumoniae ST147 strains and on a IncN-type plasmid for the K. pneumoniae ST392 strain, while blaOXA-181 gene was located on an IncX3 plasmid. All de novo assembled plasmids and plasmid-encoded transposons harboring carbapenemase genes were homologous to those previously described in the human healthcare. No plasmid replicons were detected on the OXA-48-producing E. coli ST127. The dissemination of carbapenem resistance is occurring horizontally via plasmid spreading from the human high burden carbapenem resistance setting to the companion animal sector. Furthermore, companion animals may act as reservoirs of carbapenem resistance. Implementation of carbapenemase detection methods in routine clinical veterinary microbiology is urgently needed. IMPORTANCE This is the first study on the prevalence of carbapenemase-producing Enterobacterales (CPE) clinical strains from companion animals in Portugal. Despite the generally low prevalence of CPE in companion animals, it is imperative for veterinary diagnostic laboratories to employ diagnostic methods for carbapenemase detection. The resemblance found in the mobile genetic elements transporting carbapenemase genes between veterinary medicine and human medicine implies a potential circulation within a One Health framework.
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Affiliation(s)
- Joana Moreira da Silva
- CIISA—Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, Lisbon, Portugal
- AL4AnimalS—Associate Laboratory for Animal and Veterinary Sciences, Vila Real, Portugal
| | - Juliana Menezes
- CIISA—Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, Lisbon, Portugal
- AL4AnimalS—Associate Laboratory for Animal and Veterinary Sciences, Vila Real, Portugal
| | - Laura Fernandes
- CIISA—Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, Lisbon, Portugal
- AL4AnimalS—Associate Laboratory for Animal and Veterinary Sciences, Vila Real, Portugal
| | - Sofia Santos Costa
- Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT, Universidade Nova de Lisboa, UNL, Lisbon, Portugal
| | - Andreia Amaral
- CIISA—Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, Lisbon, Portugal
- AL4AnimalS—Associate Laboratory for Animal and Veterinary Sciences, Vila Real, Portugal
| | - Constança Pomba
- CIISA—Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, Lisbon, Portugal
- AL4AnimalS—Associate Laboratory for Animal and Veterinary Sciences, Vila Real, Portugal
- Genevet, Veterinary Molecular Diagnostic Laboratory, Carnaxide, Portugal
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Escobar-Salom M, Barceló IM, Rojo-Molinero E, Jordana-Lluch E, Cabot G, Oliver A, Juan C. In vitro activity of human defensins HNP-1 and hBD-3 against multidrug-resistant ESKAPE Gram-negatives of clinical origin and selected peptidoglycan recycling-defective mutants. Microbiol Spectr 2024; 12:e0035824. [PMID: 38441982 PMCID: PMC10986477 DOI: 10.1128/spectrum.00358-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 02/20/2024] [Indexed: 03/07/2024] Open
Abstract
The use of immune compounds as antimicrobial adjuvants is a classic idea recovering timeliness in the current antibiotic resistance scenario. However, the activity of certain antimicrobial peptides against ESKAPE Gram-negatives has not been sufficiently investigated. The objective of this study was to determine the activities of human defensins HNP-1 and hBD-3 alone or combined with permeabilizing/peptidoglycan-targeting agents against clinical ESKAPE Gram-negatives [Acinetobacter baumannii (AB), Enterobacter cloacae (EC), Klebsiella pneumoniae (KP), and acute/chronic Pseudomonas aeruginosa (PA)]. Lethal concentrations (LCs) of HNP-1 and hBD-3 were determined in four collections of multidrug resistant EC, AB, KP, and PA clinical strains (10-36 isolates depending on the collection). These defensins act through membrane permeabilization plus peptidoglycan building blockade, enabling that alterations in peptidoglycan recycling may increase their activity, which is why different recycling-defective mutants were also included. Combinations with physiological lysozyme and subinhibitory colistin for bactericidal activities determination, and with meropenem for minimum inhibitory concentrations (MICs), were also assessed. HNP-1 showed undetectable activity (LC > 32 mg/L for all strains). hBD-3 showed appreciable activities: LC ranges 2-16, 8-8, 8->32, and 8->32 mg/L for AB, EC, KP, and PA, being PA strains from cystic fibrosis significantly more resistant than acute origin ones. None of the peptidoglycan recycling-defective mutants showed greater susceptibility to HNP-1/hBD-3. Combination with colistin or lysozyme did not change their bactericidal power, and virtually neither did meropenem + hBD-3 compared to meropenem MICs. This is the first study comparatively analyzing the HNP-1/hBD-3 activities against the ESKAPE Gram-negatives, and demonstrates interesting bactericidal capacities of hBD-3 mostly against AB and EC. IMPORTANCE In the current scenario of critical need for new antimicrobials against multidrug-resistant bacteria, all options must be considered, including classic ideas such as the use of purified immune compounds. However, information regarding the activity of certain human defensins against ESKAPE Gram-negatives was incomplete. This is the first study comparatively assessing the in vitro activity of two membrane-permeabilizing/peptidoglycan construction-blocking defensins (HNP-1 and hBD-3) against relevant clinical collections of ESKAPE Gram-negatives, alone or in combination with permeabilizers, additional peptidoglycan-targeting attacks, or the blockade of its recycling. Our data suggest that hBD-3 has a notable bactericidal activity against multidrug-resistant Acinetobacter baumannii and Enterobacter cloacae strains that should be considered as potential adjuvant option. Our results suggest for the first time an increased resistance of Pseudomonas aeruginosa strains from chronic infection compared to acute origin ones, and provide new clues about the predominant mode of action of hBD-3 against Gram-negatives (permeabilization rather than peptidoglycan-targeting).
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Affiliation(s)
- María Escobar-Salom
- Research Unit, University Hospital Son Espases-Health Research Institute of the Balearic Islands (IdISBa), Palma, Spain
- Microbiology Department, University Hospital Son Espases, Palma, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
| | - Isabel María Barceló
- Research Unit, University Hospital Son Espases-Health Research Institute of the Balearic Islands (IdISBa), Palma, Spain
- Microbiology Department, University Hospital Son Espases, Palma, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
| | - Estrella Rojo-Molinero
- Research Unit, University Hospital Son Espases-Health Research Institute of the Balearic Islands (IdISBa), Palma, Spain
- Microbiology Department, University Hospital Son Espases, Palma, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
| | - Elena Jordana-Lluch
- Research Unit, University Hospital Son Espases-Health Research Institute of the Balearic Islands (IdISBa), Palma, Spain
- Microbiology Department, University Hospital Son Espases, Palma, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
| | - Gabriel Cabot
- Research Unit, University Hospital Son Espases-Health Research Institute of the Balearic Islands (IdISBa), Palma, Spain
- Microbiology Department, University Hospital Son Espases, Palma, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
| | - Antonio Oliver
- Research Unit, University Hospital Son Espases-Health Research Institute of the Balearic Islands (IdISBa), Palma, Spain
- Microbiology Department, University Hospital Son Espases, Palma, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
| | - Carlos Juan
- Research Unit, University Hospital Son Espases-Health Research Institute of the Balearic Islands (IdISBa), Palma, Spain
- Microbiology Department, University Hospital Son Espases, Palma, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
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Marais G, Moodley C, Claassen-Weitz S, Patel F, Prentice E, Tootla H, Nyakutira N, Lennard K, Reddy K, Bamford C, Niehaus A, Whitelaw A, Brink A. Carbapenem-resistant Klebsiella pneumoniae among hospitalized patients in Cape Town, South Africa: molecular epidemiology and characterization. JAC Antimicrob Resist 2024; 6:dlae050. [PMID: 38529003 PMCID: PMC10963078 DOI: 10.1093/jacamr/dlae050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 03/03/2024] [Indexed: 03/27/2024] Open
Abstract
Background The molecular epidemiology of carbapenem-resistant Enterobacterales in Cape Town remains largely unknown. Objectives This study aimed to describe the molecular epidemiology, resistome, virulome and mobilome of carbapenem-resistant Klebsiella pneumoniae (CRKP) within Cape Town to guide therapy, antimicrobial stewardship and infection prevention and control practices. Methods Eighty-five CRKP isolates from hospitalized patients underwent WGS as part of a prospective, multicentre, cross-sectional study, conducted between 1 November 2020 and 30 November 2022, across public-sector and private-sector hospitals in Cape Town, South Africa. Results MLST revealed three novel types, ST6785, ST6786 and ST6787, while the most common were ST219, ST307, ST17, ST13 and ST2497. Different predominant clones were noted in each hospital. The most common carbapenemase gene was blaOXA-48-like, detected in 71% of isolates, with blaNDM detected in 5%. Notably, co-detection of two carbapenemase genes (blaOXA-48-like and blaNDM) occurred in 13% of isolates. The yersiniabactin siderophore was detected in 73% of isolates, and was most commonly associated with the ICEKp5 mobile element. All carbapenemases were located on plasmids. The genes blaOXA-181 and blaOXA-232 colocalized with a ColKP3 replicon type on assembled contigs in 83% and 100% of cases, respectively. Conclusions CRKP epidemiology in Cape Town reflects institutionally dominant, rather than regional, clones. The most prevalent carbapenemase gene was blaOXA-48-like, in keeping with CRKP epidemiology in South Africa in general. Emerging clones harbouring both blaOXA-48-like and blaNDM, such as ST17, ST2497 and the novel ST6787, are a concern due to the limited availability of appropriate antimicrobial agents in South Africa.
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Affiliation(s)
- Gert Marais
- Division of Medical Microbiology, University of Cape Town, Cape Town, Western Cape, South Africa
- National Health Laboratory Service Laboratory, Groote Schuur Hospital, Cape Town, Western Cape, South Africa
| | - Clinton Moodley
- Division of Medical Microbiology, University of Cape Town, Cape Town, Western Cape, South Africa
- National Health Laboratory Service Laboratory, Groote Schuur Hospital, Cape Town, Western Cape, South Africa
| | - Shantelle Claassen-Weitz
- Division of Medical Microbiology, University of Cape Town, Cape Town, Western Cape, South Africa
| | - Fadheela Patel
- Division of Medical Microbiology, University of Cape Town, Cape Town, Western Cape, South Africa
| | - Elizabeth Prentice
- Division of Medical Microbiology, University of Cape Town, Cape Town, Western Cape, South Africa
- National Health Laboratory Service Laboratory, Groote Schuur Hospital, Cape Town, Western Cape, South Africa
| | - Hafsah Tootla
- Division of Medical Microbiology, University of Cape Town, Cape Town, Western Cape, South Africa
- Medical Microbiology, National Health Laboratory Service, Red Cross War Memorial Children’s Hospital, Cape Town, South Africa
| | - Nyasha Nyakutira
- Division of Medical Microbiology, University of Cape Town, Cape Town, Western Cape, South Africa
| | - Katie Lennard
- Division of Computational Biology, University of Cape Town, Cape Town, Western Cape, South Africa
| | - Kessendri Reddy
- Division of Medical Microbiology, Stellenbosch University, Cape Town, Western Cape, South Africa
- National Health Laboratory Service, Tygerberg Hospital, Cape Town, Western Cape, South Africa
| | - Colleen Bamford
- Division of Medical Microbiology, University of Cape Town, Cape Town, Western Cape, South Africa
- Division of Medical Microbiology, Pathcare, Cape Town, South Africa
| | - Abraham Niehaus
- Division of Medical Microbiology, Ampath, Cape Town, South Africa
| | - Andrew Whitelaw
- Division of Medical Microbiology, Stellenbosch University, Cape Town, Western Cape, South Africa
- National Health Laboratory Service, Tygerberg Hospital, Cape Town, Western Cape, South Africa
| | - Adrian Brink
- Division of Medical Microbiology, University of Cape Town, Cape Town, Western Cape, South Africa
- National Health Laboratory Service Laboratory, Groote Schuur Hospital, Cape Town, Western Cape, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, Western Cape, South Africa
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Mendes G, Santos ML, Ramalho JF, Duarte A, Caneiras C. Virulence factors in carbapenem-resistant hypervirulent Klebsiella pneumoniae. Front Microbiol 2023; 14:1325077. [PMID: 38098668 PMCID: PMC10720631 DOI: 10.3389/fmicb.2023.1325077] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 11/16/2023] [Indexed: 12/17/2023] Open
Abstract
Hypervirulence and carbapenem-resistant have emerged as two distinct evolutionary pathotypes of Klebsiella pneumoniae, with both reaching their epidemic success and posing a great threat to public health. However, as the boundaries separating these two pathotypes fade, we assist a worrisome convergence in certain high-risk clones, causing hospital outbreaks and challenging every therapeutic option available. To better understand the basic biology of these pathogens, this review aimed to describe the virulence factors and their distribution worldwide among carbapenem-resistant highly virulent or hypervirulent K. pneumoniae strains, as well as to understand the interplay of these virulence strains with the carbapenemase produced and the sequence type of such strains. As we witness a shift in healthcare settings where carbapenem-resistant highly virulent or hypervirulent K. pneumoniae are beginning to emerge and replace classical K. pneumoniae strains, a better understanding of these strains is urgently needed for immediate and appropriate response.
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Affiliation(s)
- Gabriel Mendes
- Microbiology Research Laboratory on Environmental Health, Institute of Environmental Health (ISAMB), Associate Laboratory TERRA, Faculty of Medicine, Universidade de Lisboa, Lisbon, Portugal
| | - Maria Leonor Santos
- Microbiology Research Laboratory on Environmental Health, Institute of Environmental Health (ISAMB), Associate Laboratory TERRA, Faculty of Medicine, Universidade de Lisboa, Lisbon, Portugal
| | - João F. Ramalho
- Microbiology Research Laboratory on Environmental Health, Institute of Environmental Health (ISAMB), Associate Laboratory TERRA, Faculty of Medicine, Universidade de Lisboa, Lisbon, Portugal
| | - Aida Duarte
- Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
- Egas Moniz Center for Interdisciplinary Research, Egas Moniz School of Health and Science, Almada, Portugal
| | - Cátia Caneiras
- Microbiology Research Laboratory on Environmental Health, Institute of Environmental Health (ISAMB), Associate Laboratory TERRA, Faculty of Medicine, Universidade de Lisboa, Lisbon, Portugal
- Egas Moniz Center for Interdisciplinary Research, Egas Moniz School of Health and Science, Almada, Portugal
- Institute of Preventive Medicine and Public Health, Faculty of Medicine, Universidade de Lisboa, Lisbon, Portugal
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Emeraud C, Mahamat A, Jousset AB, Bernabeu S, Goncalves T, Pommier C, Girlich D, Birer A, Rodriguez C, Pawlotsky JM, Naas T, Bonnin RA, Dortet L. Emergence and rapid dissemination of highly resistant NDM-14-producing Klebsiella pneumoniae ST147, France, 2022. Euro Surveill 2023; 28:2300095. [PMID: 37855905 PMCID: PMC10588306 DOI: 10.2807/1560-7917.es.2023.28.42.2300095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 06/26/2023] [Indexed: 10/20/2023] Open
Abstract
BackgroundSince 2021, an emergence of New Delhi metallo-β-lactamase (NDM)-14-producing Klebsiella pneumoniae has been identified in France. This variant with increased carbapenemase activity was not previously detected in Enterobacterales.AimWe investigated the rapid dissemination of NDM-14 producers among patients in hospitals in France.MethodsAll NDM-14-producing non-duplicate clinical isolates identified in France until June 2022 (n = 37) were analysed by whole genome sequencing. The phylogeny of NDM-14-producers among all K. pneumoniae sequence type (ST) 147 reported in France since 2014 (n = 431) was performed. Antimicrobial susceptibility testing, conjugation experiments, clonal relationship and molecular clock analysis were performed.ResultsThe 37 NDM-14 producers recovered in France until 2022 belonged to K. pneumoniae ST147. The dissemination of NDM-14-producing K. pneumoniae was linked to a single clone, likely imported from Morocco and responsible for several outbreaks in France. The gene bla NDM-14 was harboured on a 54 kilobase non-conjugative IncFIB plasmid that shared high homology with a known bla NDM-1-carrying plasmid. Using Bayesian analysis, we estimated that the NDM-14-producing K. pneumoniae ST147 clone appeared in 2020. The evolutionary rate of this clone was estimated to 5.61 single nucleotide polymorphisms per genome per year. The NDM-14 producers were highly resistant to all antimicrobials tested except to colistin, cefiderocol (minimum inhibitory concentration 2 mg/L) and the combination of aztreonam/avibactam.ConclusionHighly resistant NDM-14 producing K. pneumoniae can rapidly spread in healthcare settings. Surveillance and thorough investigations of hospital outbreaks are critical to evaluate and limit the dissemination of this clone.
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Affiliation(s)
- Cécile Emeraud
- Department of Bacteriology-Hygiene, Bicêtre Hospital, Assistance Publique - Hôpitaux de Paris, Le Kremlin-Bicêtre, France
- UMR-1184, INSERM, University Paris-Saclay, CEA, Faculty of Medicine, Le Kremlin-Bicêtre, France
- French National Reference Center for Antibiotic Resistance, Le Kremlin-Bicêtre, France
| | - Aba Mahamat
- Corsica Centre for Healthcare-Associated Infections Control and Prevention, Hôpital Eugénie, Ajaccio, France
| | - Agnès B Jousset
- Department of Bacteriology-Hygiene, Bicêtre Hospital, Assistance Publique - Hôpitaux de Paris, Le Kremlin-Bicêtre, France
- UMR-1184, INSERM, University Paris-Saclay, CEA, Faculty of Medicine, Le Kremlin-Bicêtre, France
- French National Reference Center for Antibiotic Resistance, Le Kremlin-Bicêtre, France
| | - Sandrine Bernabeu
- Department of Bacteriology-Hygiene, Bicêtre Hospital, Assistance Publique - Hôpitaux de Paris, Le Kremlin-Bicêtre, France
- UMR-1184, INSERM, University Paris-Saclay, CEA, Faculty of Medicine, Le Kremlin-Bicêtre, France
| | - Tania Goncalves
- Department of Bacteriology-Hygiene, Bicêtre Hospital, Assistance Publique - Hôpitaux de Paris, Le Kremlin-Bicêtre, France
| | - Camille Pommier
- Department of Bacteriology-Hygiene, Bicêtre Hospital, Assistance Publique - Hôpitaux de Paris, Le Kremlin-Bicêtre, France
| | - Delphine Girlich
- UMR-1184, INSERM, University Paris-Saclay, CEA, Faculty of Medicine, Le Kremlin-Bicêtre, France
| | - Aurélien Birer
- Centre National de Référence de la Résistance aux antibiotiques, Service de Bactériologie, CHU Gabriel-Montpied, Clermont-Ferrand, France
| | - Christophe Rodriguez
- Université Paris-Est-Créteil (UPEC), Créteil, France
- Department of Virology, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris, Créteil, France
- INSERM U955, Team Viruses, Hepatology, Cancer, Créteil, France
| | - Jean-Michel Pawlotsky
- Université Paris-Est-Créteil (UPEC), Créteil, France
- Department of Virology, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris, Créteil, France
- INSERM U955, Team Viruses, Hepatology, Cancer, Créteil, France
| | - Thierry Naas
- Department of Bacteriology-Hygiene, Bicêtre Hospital, Assistance Publique - Hôpitaux de Paris, Le Kremlin-Bicêtre, France
- UMR-1184, INSERM, University Paris-Saclay, CEA, Faculty of Medicine, Le Kremlin-Bicêtre, France
- French National Reference Center for Antibiotic Resistance, Le Kremlin-Bicêtre, France
| | - Rémy A Bonnin
- UMR-1184, INSERM, University Paris-Saclay, CEA, Faculty of Medicine, Le Kremlin-Bicêtre, France
- French National Reference Center for Antibiotic Resistance, Le Kremlin-Bicêtre, France
| | - Laurent Dortet
- Department of Bacteriology-Hygiene, Bicêtre Hospital, Assistance Publique - Hôpitaux de Paris, Le Kremlin-Bicêtre, France
- UMR-1184, INSERM, University Paris-Saclay, CEA, Faculty of Medicine, Le Kremlin-Bicêtre, France
- French National Reference Center for Antibiotic Resistance, Le Kremlin-Bicêtre, France
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8
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Carbapenemase-Producing Klebsiella pneumoniae in COVID-19 Intensive Care Patients: Identification of IncL-VIM-1 Plasmid in Previously Non-Predominant Sequence Types. Antibiotics (Basel) 2023; 12:antibiotics12010107. [PMID: 36671308 PMCID: PMC9854421 DOI: 10.3390/antibiotics12010107] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 12/23/2022] [Accepted: 12/30/2022] [Indexed: 01/10/2023] Open
Abstract
During the COVID-19 pandemic, intensive care units (ICUs) operated at or above capacity, and the number of ICU patients coinfected by nosocomial microorganisms increased. Here, we characterize the population structure and resistance mechanisms of carbapenemase-producing Klebsiella pneumoniae (CP-Kpn) from COVID-19 ICU patients and compare them to pre-pandemic populations of CP-Kpn. We analyzed 84 CP-Kpn isolates obtained during the pandemic and 74 CP-Kpn isolates obtained during the pre-pandemic period (2019) by whole genome sequencing, core genome multilocus sequence typing, plasmid reconstruction, and antibiotic susceptibility tests. More CP-Kpn COVID-19 isolates produced OXA-48 (60/84, 71.4%) and VIM-1 (18/84, 21.4%) than KPC (8/84, 9.5%). Fewer pre-pandemic CP-Kpn isolates produced VIM-1 (7/74, 9.5%). Cefiderocol (97.3-100%) and plazomicin (97.5-100%) had the highest antibiotic activity against pandemic and pre-pandemic isolates. Sequence type 307 (ST307) was the most widely distributed ST in both groups. VIM-1-producing isolates belonging to ST307, ST17, ST321 and ST485, (STs infrequently associated to VIM-1) were detected during the COVID-19 period. Class 1 integron Int1-blaVIM-1-aac(6')-1b-dfrB1-aadAI-catB2-qacEΔ1/sul1, found on an IncL plasmid of approximately 70,000 bp, carried blaVIM-1 in ST307, ST17, ST485, and ST321 isolates. Thus, CP-Kpn populations from pandemic and pre-pandemic periods have similarities. However, VIM-1 isolates associated with atypical STs increased during the pandemic, which warrants additional monitoring and surveillance.
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9
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Harbaoui S, Ferjani S, Abbassi M, Saidani M, Gargueh T, Ferjani M, Hammi Y, Boutiba‐Ben Boubaker I. Genetic heterogeneity and predominance of
bla
CTX‐M
‐15
in cefotaxime‐resistant
Enterobacteriaceae
isolates colonizing hospitalized children in Tunisia. Lett Appl Microbiol 2022; 75:1460-1474. [DOI: 10.1111/lam.13812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 07/25/2022] [Accepted: 08/08/2022] [Indexed: 11/28/2022]
Affiliation(s)
- S. Harbaoui
- Université de Tunis El Manar, Faculté de Médecine de Tunis, LR99ES09 Laboratoire de recherche « Résistance aux antimicrobiens » 1006 Tunis Tunisie
| | - S. Ferjani
- Université de Tunis El Manar, Faculté de Médecine de Tunis, LR99ES09 Laboratoire de recherche « Résistance aux antimicrobiens » 1006 Tunis Tunisie
| | - M.S. Abbassi
- Université de Tunis El Manar, Faculté de Médecine de Tunis, LR99ES09 Laboratoire de recherche « Résistance aux antimicrobiens » 1006 Tunis Tunisie
- Université de Tunis El Manar, Institut de la recherche vétérinaire de Tunisie Tunis Tunisie
| | - M. Saidani
- Université de Tunis El Manar, Faculté de Médecine de Tunis, LR99ES09 Laboratoire de recherche « Résistance aux antimicrobiens » 1006 Tunis Tunisie
- CHU Charles Nicolle Service de Microbiologie 1006 Tunis Tunisie
| | - T. Gargueh
- CHU Charles Nicolle Service de Pédiatrie 1006 Tunis Tunisie
| | - M. Ferjani
- CHU Charles Nicolle Service de Pédiatrie 1006 Tunis Tunisie
| | - Y. Hammi
- CHU Charles Nicolle Service de Pédiatrie 1006 Tunis Tunisie
| | - I. Boutiba‐Ben Boubaker
- Université de Tunis El Manar, Faculté de Médecine de Tunis, LR99ES09 Laboratoire de recherche « Résistance aux antimicrobiens » 1006 Tunis Tunisie
- CHU Charles Nicolle Service de Microbiologie 1006 Tunis Tunisie
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10
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In Vitro and In Vivo Assessments of Two Newly Isolated Bacteriophages against an ST13 Urinary Tract Infection Klebsiella pneumoniae. Viruses 2022; 14:v14051079. [PMID: 35632820 PMCID: PMC9144312 DOI: 10.3390/v14051079] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/09/2022] [Accepted: 05/13/2022] [Indexed: 12/11/2022] Open
Abstract
Antibiotic resistance represents a major public health concern requiring new alternatives including phage therapy. Klebsiella pneumoniae belongs to the ESKAPE bacteria and can cause urinary tract infections (UTIs). The aims of this study were to isolate and characterize new bacteriophages against a K. pneumoniae strain isolated from UTIs and to assess their efficacy in vitro and in vivo in a Galleria (G.) mellonella larvae model. For this purpose, two bacteriophages were newly isolated against an ST13 K. pneumoniae strain isolated from a UTI and identified as K3 capsular types by wzi gene PCR. Genomic analysis showed that these bacteriophages, named vB_KpnP_K3-ULINTkp1 and vB_KpnP_K3-ULINTkp2, belong to the Drulisvirus genus. Bacteriophage vB_KpnP_K3-ULINTkp1 had the narrowest host spectrum (targeting only K3), while vB_KpnP_K3-ULINTkp2 also infected other Klebsiella types. Short adsorption times and latent periods were observed for both bacteriophages. In vivo experiments showed their ability to replicate in G. mellonella larvae and to decrease host bacterial titers. Moreover, both bacteriophages improved the survival of the infected larvae. In conclusion, these two bacteriophages had different in vitro properties and showed in vivo efficacy in a G. mellonella model with a better efficiency for vB_KpnP_K3-ULINTkp2.
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11
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Kvesić M, Šamanić I, Novak A, Fredotović Ž, Dželalija M, Kamenjarin J, Goić Barišić I, Tonkić M, Maravić A. Submarine Outfalls of Treated Wastewater Effluents are Sources of Extensively- and Multidrug-Resistant KPC- and OXA-48-Producing Enterobacteriaceae in Coastal Marine Environment. Front Microbiol 2022; 13:858821. [PMID: 35602062 PMCID: PMC9121779 DOI: 10.3389/fmicb.2022.858821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 04/06/2022] [Indexed: 11/13/2022] Open
Abstract
The rapid and ongoing spread of carbapenemase-producing Enterobacteriaceae has led to a global health threat. However, a limited number of studies have addressed this problem in the marine environment. We investigated their emergence in the coastal waters of the central Adriatic Sea (Croatia), which are recipients of submarine effluents from two wastewater treatment plants. Fifteen KPC-producing Enterobacteriaceae (nine Escherichia coli, four Klebsiella pneumoniae and two Citrobacter freundii) were recovered, and susceptibility testing to 14 antimicrobials from 10 classes showed that four isolates were extensively drug resistant (XDR) and two were resistant to colistin. After ERIC and BOX-PCR typing, eight isolates were selected for whole genome sequencing. The E. coli isolates belonged to serotype O21:H27 and sequence type (ST) 2795, while K. pneumoniae isolates were assigned to STs 37 and 534. Large-scale genome analysis revealed an arsenal of 137 genes conferring resistance to 19 antimicrobial drug classes, 35 genes associated with virulence, and 20 plasmid replicons. The isolates simultaneously carried 43–90 genes encoding for antibiotic resistance, while four isolates co-harbored carbapenemase genes blaKPC-2 and blaOXA-48. The blaOXA-48 was associated with IncL-type plasmids in E. coli and K. pneumoniae. Importantly, the blaKPC-2 in four E. coli isolates was located on ~40 kb IncP6 broad-host-range plasmids which recently emerged as blaKPC-2 vesicles, providing first report of these blaKPC-2-bearing resistance plasmids circulating in E. coli in Europe. This study also represents the first evidence of XDR and potentially virulent strains of KPC-producing E. coli in coastal waters and the co-occurrence of blaKPC-2 and blaOXA-48 carbapenemase genes in this species. The leakage of these strains through submarine effluents into coastal waters is of concern, indicating a reservoir of this infectious threat in the marine environment.
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Affiliation(s)
- Marija Kvesić
- Center of Excellence for Science and Technology, Integration of Mediterranean Region, University of Split, Split, Croatia
- Doctoral Study of Biophysics, Faculty of Science, University of Split, Split, Croatia
| | - Ivica Šamanić
- Department of Biology, Faculty of Science, University of Split, Split, Croatia
| | - Anita Novak
- School of Medicine, University of Split, Split, Croatia
- University Hospital Split, Split, Croatia
| | - Željana Fredotović
- Department of Biology, Faculty of Science, University of Split, Split, Croatia
| | - Mia Dželalija
- Department of Biology, Faculty of Science, University of Split, Split, Croatia
| | - Juraj Kamenjarin
- Department of Biology, Faculty of Science, University of Split, Split, Croatia
| | - Ivana Goić Barišić
- School of Medicine, University of Split, Split, Croatia
- University Hospital Split, Split, Croatia
| | - Marija Tonkić
- School of Medicine, University of Split, Split, Croatia
- University Hospital Split, Split, Croatia
| | - Ana Maravić
- Department of Biology, Faculty of Science, University of Split, Split, Croatia
- *Correspondence: Ana Maravić,
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