Epidemiologia molecular e estudo dos determinantes genéticos de resistência e virulência em isolados clínicos de Klebsiella spp.

Associação para o Desenvolvimento do Ensino e Investigação em Microbiologia (ADEIM), Faculdade de Farmácia da Universidade de Lisboa; Instituto de Investigação do Medicamento (iMed.ULisboa

Hafnia alvei Pneumonia: a rare cause of infection in a patient with COVID-19

© 2021 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).Herein, we describe a case report of a critically ill patient, a 48-year-old man without comorbidities admitted to the hospital with a serious type 1 (hypoxemic) respiratory insufficiency and confirmed diagnosis of COVID-19. After 5 days with invasive mechanical ventilation, the patient developed a bacterial co-infection, namely a pneumonia by Hafnia alvei, requiring the last line of respiratory support: extracorporeal membrane oxygenation (ECMO). Subsequently, his clinical situation gradually stabilized, until he was discharged from the hospital on day 61, being accompanied in ambulatory consultation by the physical medicine and pulmonology department during the post-COVID-19 recovery. H. alvei is a Gram-negative bacterium that is rarely isolated from human specimens and is rarely considered to be pathogenic. However, COVID-19 disease can cause substantial organ dysfunction and can be associated with bacterial secondary infections which can favor the emergence of rare infectious diseases by uncommon microorganisms.info:eu-repo/semantics/publishedVersio

Measurement properties of step tests for exercise capacity in COPD : a systematic review

© The Author(s) 2020. This article is distributed under the terms of the Creative Commons Attribution-NonCommercial 4.0 License (https://creativecommons.org/licenses/by-nc/4.0/) which permits non-commercial use, reproduction and distribution of the work without further permission provided the original work is attributed as specified on the SAGE and Open Access page (https://us.sagepub.com/en-us/nam/open-access-at-sage).Objective: To determine the level of evidence of the measurement properties (validity, reliability, and responsiveness) and interpretability of the step tests available for assessing the exercise capacity in patients with chronic obstructive pulmonary disease. Data sources: The data sources Web of Science, MEDLINE, PubMed, PEDro, CENTRAL of Cochrane Library, and Scopus were searched up to June 26, 2020. Review methods: Studies of any design that reported results for any measurement property of the step tests for assessing the exercise capacity in COPD patients were selected. One reviewer extracted the data, and two reviewers independently rated the level of evidence by using the Consensus-Based Standards for the Selection of Health Measurements Instruments recommendations. Results: Thirty-one studies were included in the data synthesis. Chester Step Test, Modified Incremental Step Test, two-, three-, four-, and six-Minute Step Test, Paced Step Test, and six-Minute Stepper Test were identified. A step test protocol was also found. The level of evidence of their results for the measurement properties was mostly determined as “low” to “very low.” The best level of evidence found was for the six-minute stepper test: “high” on construct validity (r = 0.56–0.71); and “moderate” on criterion validity (r = 0.36–0.69), and responsiveness (r = 0.26–0.34). Conclusion: The general level of evidence of the measurement properties of the step tests is “low” to “very low” for assessing exercise capacity in patients with chronic obstructive pulmonary disease, which can limit their application in clinical practice. The six-minute Stepper Test is currently the most appropriate step test available.info:eu-repo/semantics/publishedVersio

From inception to implementation: strategies for setting up pulmonary telerehabilitation

Copyright © 2022 Santos, Rodrigues, Caneiras and Bárbara. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.Smaug is a conserved translational regulator that binds numerous mRNAs, including nuclear transcripts that encode mitochondrial enzymes. Smaug orthologs form cytosolic membrane-less organelles (MLOs) in several organisms and cell types. We have performed single-molecule fluorescence in situ hybridization (FISH) assays that revealed that SDHB and UQCRC1 mRNAs associate with Smaug1 bodies in U2OS cells. Loss of function of Smaug1 and Smaug2 (also known as SAMD4A and SAMD4B, respectively) affected both mitochondrial respiration and morphology of the mitochondrial network. Phenotype rescue by Smaug1 transfection depends on the presence of its RNA-binding domain. Moreover, we identified specific Smaug1 domains involved in MLO formation, and found that impaired Smaug1 MLO condensation correlates with mitochondrial defects. Mitochondrial complex I inhibition upon exposure to rotenone, but not strong mitochondrial uncoupling upon exposure to CCCP, rapidly induced the dissolution of Smaug1 MLOs. Metformin and rapamycin elicited similar effects, which were blocked by pharmacological inhibition of AMP-activated protein kinase (AMPK). Finally, we found that Smaug1 MLO dissolution weakens the interaction with target mRNAs, thus enabling their release. We propose that mitochondrial respiration and the AMPK-mTOR balance controls the condensation and dissolution of Smaug1 MLOs, thus regulating nuclear mRNAs that encode key mitochondrial proteins. This article has an associated First Person interview with the first authors of the paper.This work was supported by Fundação para a Ciência e Tecnologia (FCT) and Nippon Gases Portugal under the Ph.D. studentship in Industry grant PDE/BDE/127785/2016 awarded to CS.info:eu-repo/semantics/publishedVersio

Community- and hospital-acquired Klebsiella pneumoniae urinary tract infections in Portugal : virulence and antibiotic resistance

© 2019 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).Klebsiella pneumoniae is a clinically relevant pathogen and a frequent cause of hospital-acquired (HA) and community-acquired (CA) urinary tract infections (UTI). The increased resistance of this pathogen is leading to limited therapeutic options. To investigate the epidemiology, virulence, and antibiotic resistance profile of K. pneumoniae in urinary tract infections, we conducted a multicenter retrospective study for a total of 81 isolates (50 CA-UTI and 31 HA-UTI) in Portugal. The detection and characterization of resistance and virulence determinants were performed by molecular methods (PCR, PCR-based replicon typing, and multilocus sequence typing (MLST)). Out of 50 CA-UTI isolates, six (12.0%) carried β-lactamase enzymes, namely blaTEM-156 (n = 2), blaTEM-24 (n = 1), blaSHV-11 (n = 1), blaSHV-33 (n = 1), and blaCTX-M-15 (n = 1). All HA-UTI were extended-spectrum β-lactamase (ESBL) producers and had a multidrug resistant profile as compared to the CA-UTI isolates, which were mainly resistant to ciprofloxacin, levofloxacin, tigecycline, and fosfomycin. In conclusion, in contrast to community-acquired isolates, there is an overlap between virulence and multidrug resistance for hospital-acquired UTI K. pneumoniae pathogens. The study is the first to report different virulence characteristics for hospital and community K. pneumoniae pathogens, despite the production of β-lactamase and even with the presence of CTX-M-15 ESBL, a successful international ST15 clone, which were identified in both settings. This highlights that a focus on genomic surveillance should remain a priority in the hospital environment.This research was funded by the Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa (ULisboa).info:eu-repo/semantics/publishedVersio

Virulence factors in carbapenem-resistant hypervirulent Klebsiella pneumoniae

Copyright © 2023 Mendes, Santos, Ramalho, Duarte and Caneiras. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.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 carbapenemresistant 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.This research was partially funded by Fundação para a Ciência e a Tecnologia (FCT), under grant numbers UIDB/04295/2020 and UIDP/04295/2020. Moreover, CC acknowledges the funding provided by the “Research Award in Healthcare Associated Infections” granted by Escola Superior de Saúde Norte da Cruz Vermelha Portuguesa (2019) and by “BInov award,” an innovation award granted by the Southern Regional Section and Autonomous Regions of the Portuguese Pharmaceutical Society (2021). GM was supported by Fundação para a Ciência e Tecnologia (FCT), Portugal, through a Ph.D. Research Studentship Contract (Contrato de Bolsa de Investigação para Doutoramento 2020.07736.BD).info:eu-repo/semantics/publishedVersio

First outbreak of NDM-1-producing Klebsiella pneumoniae ST11 in a Portuguese hospital centre during the COVID-19 pandemic

© 2022 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).New Delhi metallo-β-lactamase (NDM) carbapenemase has been considered a global threat due to its worldwide widespread in recent years. In Portugal, a very low number of infections with NDM-producing Enterobacterales has been reported. A total of 52 strains from 40 patients and 1 environmental sample isolated during COVID-19 pandemic were included in this study. Wholegenome sequencing (WGS) was performed on 20 carbapenemase-producing strains, including 17 NDM-1-producing Klebsiella pneumoniae ST11-KL105 lineage strains, one NDM-1-producing Escherichia coli ST58 strain and one KPC-3-producing K. pneumoniae ST147 strain, recovered from a total of 19 patients. Of interest, also one NDM-1-producing K. pneumoniae ST11-KL105 was collected from the hospital environment. Genome-wide phylogenetic analysis revealed an ongoing dissemination of NDM-1-producing K. pneumoniae ST11 strains (n = 18) with the same genetic features seen across multiple wards. Furthermore, the ST58 E. coli strain, collected from a patient rectal swab that was also colonised with a K. pneumoniae strain, also showed the IncFIA plasmid replicon and the blaNDM-1 gene (preceded by IS30 and followed by genes bleMBL, trpF, dsbC, cutA, groES and groEL). The blaNDM-1 is part of Tn125-like identical to those reported in Poland, Italy and India. The blaKPC-3 K. pneumoniae ST147-KL64 strain has the genetic environment Tn4401d isoform. In conclusion, herein we report the molecular epidemiology, resistome, virulome and mobilome of the first NDM-1 carbapenemase outbreak caused by K. pneumoniae ST11-KL105 lineage during the COVID-19 pandemic in Portugal. Moreover, the outbreak strains characterised included seventeen different patients (infected and colonised) and one environmental sample which also emphasises the role of commensal and hospital environment strains in the dissemination of the outbreak.This research was partially funded by Fundação para a Ciência e a Tecnologia (FCT), grant number UIDB/04295/2020 and UIDP/04295/2020. Moreover, Cátia Caneiras (C.C.) acknowledge the funding provided by the “Research Award in Healthcare-associated Infections” granted by Escola Superior de Saúde Norte da Cruz Vermelha Portuguesa (2019) and by “BInov award”, an Innovation award granted by Southern Regional and Autonomous Regions Section of the Portuguese Pharmaceutical Society(2021). Gabriel Mendes (G.M.) is supported by Fundação para a Ciência e Tecnologia (FCT), Portugal, through PhD Research Studentship Contract (Contrato de Bolsa de Investigação para Doutoramento 2020.07736.BD).info:eu-repo/semantics/publishedVersio

Photo-realistic interactive virtual environments for neurorehabilitation in mild cognitive impairment (NeuroVRehab.PT) : a participatory design and proof-of-concept study

© 2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).Mild cognitive impairment (MCI) is characterized by cognitive, psychological, and functional impairments. Digital interventions typically focus on cognitive deficits, neglecting the difficulties that patients experience in instrumental activities of daily living (IADL). The global conjecture created by COVID-19 has highlighted the seminal importance of digital interventions for the provision of healthcare services. Here, we investigated the feasibility and rehabilitation potential of a new design approach for creating highly realistic interactive virtual environments for MCI patients' neurorehabilitation. Through a participatory design protocol, a neurorehabilitation digital platform was developed using images captured from a Portuguese supermarket (NeuroVRehab.PT). NeuroVRehab.PT's main features (e.g., medium-sized supermarket, the use of shopping lists) were established according to a shopping behavior questionnaire filled in by 110 older adults. Seven health professionals used the platform and assessed its rehabilitation potential, clinical applicability, and user experience. Interviews were conducted using the think-aloud method and semi-structured scripts, and four main themes were derived from an inductive semantic thematic analysis. Our findings support NeuroVRehab.PT as an ecologically valid instrument with clinical applicability in MCI neurorehabilitation. Our design approach, together with a comprehensive analysis of the patients' past experiences with IADL, is a promising technique to develop effective digital interventions to promote real-world functioning.TThis research was carried out as part of the doctoral studies of the first author (Ref: PDE/BDE/127784/2016) and for which she received scholarships from the following entities: Nippon Gases Portugal and Fundação para a Ciência e a Tecnologia through the European Social Fund and Human Capital Operational Programme, co-financed by Portugal 2020 and European Union. The work was partially supported by LASIGE Research Unit, ref. UIDB/00408/2020 and ref. UIDP/00408/2020.info:eu-repo/semantics/publishedVersio

Effects of a home-based pulmonary rehabilitation program in patients with chronic obstructive pulmonary disease in GOLD B group : a pilot study

© 2021 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).Patients with chronic obstructive pulmonary disease (COPD) in the Global Initiative for Chronic Obstructive Lung Disease (GOLD) B group can be included in pulmonary rehabilitation (PR) settings outside the hospitals. This study aimed to explore the feasibility of a home-based pulmonary rehabilitation (HBPR) program and assess its impact on patients with COPD in the GOLD B group. A real-world, pre-post intervention study was conducted with 12 weeks of HBPR (presential home visits and phone calls) using the self-management program Living Well with COPD. The 1-min sit-to-stand test (1MSTS), modified Medical Research Council Questionnaire (mMRC), COPD Assessment Test (CAT), Hospital Anxiety and Depression Scale (HADS), and London Chest Activity of Daily Living (LCADL) were used to assess the impact. Pre-post differences and correlations between changes in outcomes were calculated. In 30 patients (71.6 years, FEV1 (%) 52.8), significant improvements (p < 0.05) were observed on 1MSTS (Pre 17.2, Post 21.2), mMRC (Pre 2.0, Post 1.0), CAT (Pre 16.3, Post 9.9), HADS (Pre 14.4, Post 9.6), and LCADL (Pre 21.0, Post 15.8), with no adverse events reported. When significant, correlations between changes in outcomes were moderate or strong (0.48 ≤ ρ ≤ 0.66). HBPR can be feasible and safe, and it shows the potential to significantly improve outcomes of patients with COPD in the GOLD B group.info:eu-repo/semantics/publishedVersio

Whole-genome sequencing enables molecular characterization of non-clonal group 258 high-risk clones (ST13, ST17, ST147 and ST307) among Carbapenem-resistant Klebsiella pneumoniae from a tertiary university hospital centre in Portugal

© 2022 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).The carbapenem-resistant Enterobacterales (CRE) strains have been identified by the World Health Organization as critical priority pathogens in research and development of diagnostics, treatments, and vaccines. However, recent molecular information about carbapenem-resistant K. pneumoniae (CRK) epidemiology in Portugal is still scarce. Thus, this study aimed to provide the molecular epidemiology, resistome, and virulome of CRK clinical strains recovered from a tertiary care hospital centre (2019–2021) using polymerase chain reaction (PCR) and the advanced molecular technique whole-genome sequencing (WGS). PCR amplification of carbapenemase genes was performed in 437 carbapenem-resistant K. pneumoniae strains. The most frequent carbapenemases were: KPC-3 (42%), followed by OXA-181 (20%), GES-5 (0.2%), and NDM-1 (0.2%). Additionally, 10 strains (2%) coproduced KPC-3 and OXA-181, and 1 strain coproduced KPC-3 and OXA-48 (0.2%). The genomic population structure of 68 strains characterized by WGS demonstrated the ongoing dissemination of four main high-risk clones: ST13, ST17, ST147, and ST307, while no clones belonging to the European predominant clonal groups (CG15 and CG258) were found. Moreover, we describe one K. pneumoniae ST39-KL62 that coproduced the NDM-1 carbapenemase and the extended-spectrum beta-lactamase CTX-M-15, and one K. pneumoniae ST29-KL54 GES-5 and BEL-1 coproducer. Furthermore, a high prevalence of iron siderophores were present in all CRK strains, with several strains presenting both colibactin and the hypermucoviscosity phenotype. Thus, the data presented here highlight an uncommon molecular epidemiology pattern in Portugal when compared with most European countries, further supporting the emergence and dissemination of nonclonal group 258 hypervirulent multidrug high-risk clones and the need to promote in-depth hospital molecular surveillance studies.This research was partially funded by Fundação para a Ciência e a Tecnologia (FCT), under grant numbers UIDB/04295/2020 and UIDP/04295/2020. Moreover, Cátia Caneiras (C.C.) acknowledges the funding provided by the “Research Award in Healthcare Associated Infections” granted by Escola Superior de Saúde Norte da Cruz Vermelha Portuguesa (2019) and by “BInov award”, an innovation award granted by the Southern Regional Section and Autonomous Regions of the Portuguese Pharmaceutical Society (2021). Gabriel Mendes (G.M.) was supported by Fundação para a Ciência e Tecnologia (FCT), Portugal, through a PhD Research Studentship Contract (Contrato de Bolsa de Investigação para Doutoramento 2020.07736.BD).info:eu-repo/semantics/publishedVersio