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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:S0195-6701(24)00106-3. [PMID: 38554808 DOI: 10.1016/j.jhin.2024.02.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [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 complex (CR-KP) are a public health concern, causing infections with a high mortality rate, limited therapeutic options and challenging infection control strategies. In Portugal CR-KP rate has increased steeply, but the factors associated to this expansion are poorly explored. To address this question we compared, by phylogenetic and resistome analysis, the draft genomes of 200 CR-KP isolates collected in 2017-2019 from five hospitals in the Lisbon region, Portugal. We found that CR-KP belonged mainly to ST13 (29%), ST17 (15%), ST348 (13%), ST231 (12%) and ST147 (7%). Carbapenem resistance was conferred mostly by KPC-3 (74%) or OXA-181 (18%) presence, which were associated with IncF/IncN and IncX plasmids, respectively. Almost all isolates were multidrug resistant harbouring resistance determinants to aminoglycosides, beta-lactams, trimethoprim, fosfomycin, quinolones and sulphonamides. In addition, 11% of isolates were resistant to colistin. Colonizing and infection isolates were highly related and most colonized patients (89%) reported a previous hospitalization. Moreover, among the 171 events of cross-dissemination identified, by cgMLST data analysis (<5 alleles), 41 occurred between different hospitals and 130 within the same hospital. Our results suggest that CR-KP dissemination in the Lisbon region result 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. Our data reinforces that the prudent use of carbapenems, patients screening at hospital entrance, and improvement of infection control will be needed to decrease the burden of CR-KP infection in Portugal.
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Affiliation(s)
- Nuno Alexandre Faria
- Laboratory of Bacterial Evolution and Molecular Epidemiology, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa; Laboratory of Molecular Genetics, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa
| | - Tiago Touret
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa
| | - Alexandra S Simões
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa
| | | | | | | | - Mário Ramirez
- Centro Hospitalar Lisboa Norte; Instituto de Microbiologia, Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa
| | - João Carriço
- Centro Hospitalar Lisboa Norte; Instituto de Microbiologia, Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa
| | | | | | | | | | | | - Mariana Araújo
- Laboratory of Bacterial Evolution and Molecular Epidemiology, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa
| | - Aida Duarte
- Faculdade de Farmácia, Universidade de Lisboa; Centro de investigação Interdisciplinar Egas Moniz, Instituto Universitário Egas Moniz
| | - Hermínia de Lencastre
- Laboratory of Molecular Genetics, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa; Laboratory of Microbiology and Infectious Diseases, The Rockefeller University, New York, New York
| | - Mónica Serrano
- Laboratory of Microbial Development, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa
| | - Raquel Sá-Leão
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa
| | - Maria Miragaia
- Laboratory of Bacterial Evolution and Molecular Epidemiology, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa.
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Félix S, Handem S, Nunes S, Paulo AC, Candeias C, Valente C, Simões AS, Almeida ST, Tavares DA, Brito-Avô A, de Lencastre H, Sá-Leão R. Impact of private use of the 13-valent pneumococcal conjugate vaccine (PCV13) on pneumococcal carriage among Portuguese children living in urban and rural regions. Vaccine 2021; 39:4524-4533. [PMID: 34183206 DOI: 10.1016/j.vaccine.2021.06.035] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 05/27/2021] [Accepted: 06/14/2021] [Indexed: 10/21/2022]
Abstract
In Portugal, the 13-valent pneumococcal conjugate vaccine (PCV13) was commercially available between 2010 and 2015, following a decade of private use of PCV7. We evaluated changes on serotype distribution and antimicrobial susceptibility of pneumococci carried by children living in two regions of Portugal (one urban and one rural). Three epidemiological periods were defined: pre-PCV13 (2009-2010), early-PCV13 (2011-2012), and late-PCV13 (2015-2016). Nasopharyngeal samples (n = 4,232) were obtained from children 0-6 years old attending day-care centers. Private use of PCVs was very high in both regions (>75%). Pneumococcal carriage remained stable and high over time (62.1%, 62.4% and 61.6% (p = 0.909) in the urban region; and 59.8%, 62.8%, 59.5% (p = 0.543) in the rural region). Carriage of PCV7 serotypes remained low (5.3%, 7.8% and 4.3% in the urban region; and 2.5%, 3.7% and 4.8% in the rural region). Carriage of PCV13 serotypes not targeted by PCV7 decreased in both the urban (16.4%, 7.3%, and 1.6%; p < 0.001) and rural regions (13.2%, 7.8%, and 1.9%; p < 0.001). This decline was mostly attributable to serotype 19A (14.1%, 4.4% and 1.3% in the urban region; and 11.1%, 3.6% and 0.8% in the rural region, both p < 0.001). Serotype 3 declined over time in the urban region (10.1%, 4.4%, 0.8%; p < 0.001) and had no obvious trend in the rural region (4.2%, 6.7%, 2.4%; p = 0.505). Serotype 6C decreased in both regions while serotypes 11D, 15A/B/C, 16F, 21, 22F, 23A/B, 24F, 35F, and NT were the most prevalent in the late-PCV13 period. Intermediate resistance to penicillin and non-susceptibility to erythromycin decreased significantly in both regions (19.5%, 13.3%, and 9.3%; and 25.4%, 25.9%, and 13.4%; both p < 0.001, respectively in the urban region; and 12.4%, 11.1%, and 2.8% (p < 0.001); and 15.3%, 14.7%, and 9.2% (p = 0.037), respectively, in the rural region). In conclusion, private use of PCV13 led to significant changes on the pneumococcal population carried by children in Portugal.
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Affiliation(s)
- Sofia Félix
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Oeiras, Portugal
| | - Sara Handem
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Oeiras, Portugal
| | - Sónia Nunes
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Oeiras, Portugal
| | - Ana Cristina Paulo
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Oeiras, Portugal
| | - Catarina Candeias
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Oeiras, Portugal
| | - Carina Valente
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Oeiras, Portugal
| | - Alexandra S Simões
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Oeiras, Portugal
| | - Sónia T Almeida
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Oeiras, Portugal
| | - Débora A Tavares
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Oeiras, Portugal
| | | | - Hermínia de Lencastre
- Laboratory of Molecular Genetics, ITQB NOVA, Oeiras, Portugal; Laboratory of Microbiology and Infectious Diseases, The Rockefeller University, NY, USA
| | - Raquel Sá-Leão
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Oeiras, Portugal.
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Simões AS, Maia MR, Gregório J, Couto I, Asfeldt AM, Simonsen GS, Póvoa P, Viveiros M, Lapão LV. Participatory implementation of an antibiotic stewardship programme supported by an innovative surveillance and clinical decision-support system. J Hosp Infect 2018; 100:257-264. [PMID: 30071264 DOI: 10.1016/j.jhin.2018.07.034] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 07/24/2018] [Indexed: 10/28/2022]
Abstract
BACKGROUND Antibiotic resistance will cause about 10 million deaths per year by 2050. Fighting antimicrobial resistance is a health priority. Interventions aimed to reduce antimicrobial resistance, such as antibiotic stewardship programmes (ASPs), must be implemented. To be effective, those interventions, and the implementation process, should be matched with social-cultural context. The complexity of ASPs can no longer be developed without considering both organizational and information systems. AIM To support ASPs through the co-design and implementation, in collaboration with healthcare workers, of a surveillance and clinical decision-support system to monitor antibiotic resistance and improve antibiotic prescription. METHODS The surveillance and clinical decision-support system was designed and implemented in three Portuguese hospitals, using a participatory approach between researchers and healthcare workers following the Design Science Research Methodology. FINDINGS Based on healthcare workers' requirements, we developed HAITooL, a real-time surveillance and clinical decision-support system that integrates visualizations of patient, microbiology, and pharmacy data, facilitating clinical decision. HAITooL monitors antibiotic usage and rates of antibiotic-resistant bacteria, allowing early identification of outbreaks. It is a clinical decision-support tool that integrates evidence-based algorithms to support proper antibiotic prescription. HAITooL was considered valuable to support monitoring of antibiotic resistant infections and an important tool for ASP sustainability. CONCLUSION ASP implementation can be leveraged through a surveillance and clinical decision-support system such as HAITooL that allows antibiotic resistance monitoring and supports antibiotic prescription, once it has been adapted to the context and specific needs of healthcare workers and hospitals.
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Affiliation(s)
- A S Simões
- Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal
| | - M R Maia
- Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal
| | - J Gregório
- Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal
| | - I Couto
- Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal
| | - A M Asfeldt
- University Hospital of North Norway and UiT - Arctic University of Norway, Tromsø, Norway
| | - G S Simonsen
- University Hospital of North Norway and UiT - Arctic University of Norway, Tromsø, Norway
| | - P Póvoa
- NOVA Medical School, CEDOC, Universidade Nova de Lisboa, Lisbon, Portugal; Polyvalent Intensive Care Unit, São Francisco Xavier Hospital, Centro Hospitalar de Lisboa Ocidental, Lisbon, Portugal
| | - M Viveiros
- Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal
| | - L V Lapão
- Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal.
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Simões AS, Alves DA, Gregório J, Couto I, Dias S, Póvoa P, Viveiros M, Gonçalves L, Lapão LV. Fighting antibiotic resistance in Portuguese hospitals: Understanding antibiotic prescription behaviours to better design antibiotic stewardship programmes. J Glob Antimicrob Resist 2018; 13:226-230. [PMID: 29409949 DOI: 10.1016/j.jgar.2018.01.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 12/27/2017] [Accepted: 01/19/2018] [Indexed: 10/18/2022] Open
Abstract
OBJECTIVES Since physicians play an important role in antibiotic usage, it is vital to understand their antibiotic-prescribing behaviour and knowledge on antimicrobial resistance in order to develop and implement effective antibiotic stewardship interventions. The aim of this study was to evaluate Portuguese physicians' knowledge and to understand prescription behaviours, difficulties and barriers in their antibiotic prescription process in order to promote better and well-adapted antibiotic stewardship policies. METHODS This study was conducted in 2016 using a self-administered questionnaire to physicians in two tertiary public hospitals from two different regions in Portugal. RESULTS Participating physicians [response rate 47.6% (30/63)] identified antibiotic resistance as a global problem; however, one-third did not recognise antibiotic resistance as a major problem on their own hospital. Factors that most influenced antibiotic prescription were 'microbiology laboratory results', 'patient clinical situation' and patient 'co-morbidities'. On the other hand, 'colleagues' opinion' and 'costs control' were considered as less determining factors. Regarding difficulties and bottlenecks in the antibiotic prescription process, participant physicians reported 'lack of (or delayed) microbiological results' and 'no access to antibiotic susceptibility patterns' as major barriers. 'Education and training' was considered the most effective intervention to improve antibiotic prescription. CONCLUSION These results suggest that the design and implementation of antibiotic stewardship interventions should provide better data management and sharing tools between physicians and the microbiology laboratory, especially through the creation of antimicrobial prescribing guidelines according to hospital epidemiology, and easy access to hospital antibiotic susceptibility patterns and epidemiological data.
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Affiliation(s)
- Alexandra S Simões
- Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa (UNL), Rua da Junqueira no 100, 1349-008 Lisbon, Portugal.
| | - Daniela A Alves
- Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa (UNL), Rua da Junqueira no 100, 1349-008 Lisbon, Portugal
| | - João Gregório
- Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa (UNL), Rua da Junqueira no 100, 1349-008 Lisbon, Portugal
| | - Isabel Couto
- Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa (UNL), Rua da Junqueira no 100, 1349-008 Lisbon, Portugal
| | - Sónia Dias
- Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa (UNL), Rua da Junqueira no 100, 1349-008 Lisbon, Portugal
| | - Pedro Póvoa
- CEDOC, NOVA Medical School, UNL, Lisbon, Portugal; Unidade de Cuidados Intensivos Polivalente, Hospital de São Francisco Xavier, Centro Hospitalar de Lisboa Ocidental, Lisbon, Portugal
| | - Miguel Viveiros
- Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa (UNL), Rua da Junqueira no 100, 1349-008 Lisbon, Portugal
| | - Luzia Gonçalves
- Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa (UNL), Rua da Junqueira no 100, 1349-008 Lisbon, Portugal; Centro de Estatística e Aplicações da Universidade de Lisboa, Lisbon, Portugal
| | - Luís V Lapão
- Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa (UNL), Rua da Junqueira no 100, 1349-008 Lisbon, Portugal
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Simões AS, Couto I, Toscano C, Gonçalves E, Póvoa P, Viveiros M, Lapão LV. Prevention and Control of Antimicrobial Resistant Healthcare-Associated Infections: The Microbiology Laboratory Rocks! Front Microbiol 2016; 7:855. [PMID: 27375577 PMCID: PMC4895126 DOI: 10.3389/fmicb.2016.00855] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 05/23/2016] [Indexed: 12/30/2022] Open
Abstract
In Europe, each year, more than four milion patients acquire a healthcare-associated infection (HAI) and almost 40 thousand die as a direct consequence of it. Regardless of many stategies to prevent and control HAIs, they remain an important cause of morbidity and mortality worldwide with a significant economic impact: a recent estimate places it at the ten billion dollars/year. The control of HAIs requires a prompt and efficient identification of the etiological agent and a rapid communication with the clinician. The Microbiology Laboratory has a significant role in the prevention and control of these infections and is a key element of any Infection Control Program. The work of the Microbiology Laboratory covers microbial isolation and identification, determination of antimicrobial susceptibility patterns, epidemiological surveillance and outbreak detection, education, and report of quality assured results. In this paper we address the role and importance of the Microbiology Laboratory in the prevention and control of HAI and in Antibiotic Stewardship Programs and how it can be leveraged when combined with the use of information systems. Additionally, we critically review some challenges that the Microbiology Laboratory has to deal with, including the selection of analytic methods and the proper use of communication channels with other healthcare services.
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Affiliation(s)
- Alexandra S. Simões
- Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, LisbonPortugal
| | - Isabel Couto
- Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, LisbonPortugal
| | - Cristina Toscano
- Laboratório de Microbiologia Clínica e Biologia Molecular, Serviço de Patologia Clínica, Hospital de Egas Moniz, Centro Hospitalar de Lisboa Ocidental, LisbonPortugal
- Centro de Estudos de Doenças Crónicas, NOVA Medical School/Faculdade de Ciências Médicas, Universidade Nova de Lisboa, LisbonPortugal
| | - Elsa Gonçalves
- Laboratório de Microbiologia Clínica e Biologia Molecular, Serviço de Patologia Clínica, Hospital de Egas Moniz, Centro Hospitalar de Lisboa Ocidental, LisbonPortugal
- Centro de Estudos de Doenças Crónicas, NOVA Medical School/Faculdade de Ciências Médicas, Universidade Nova de Lisboa, LisbonPortugal
| | - Pedro Póvoa
- Centro de Estudos de Doenças Crónicas, NOVA Medical School/Faculdade de Ciências Médicas, Universidade Nova de Lisboa, LisbonPortugal
- Unidade de Cuidados Intensivos Polivalente, Hospital de São Francisco Xavier, Centro Hospitalar de Lisboa Ocidental, LisbonPortugal
| | - Miguel Viveiros
- Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, LisbonPortugal
| | - Luís V. Lapão
- Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, LisbonPortugal
- WHO Collaborating Center for Health Workforce Policy and Planning, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, LisbonPortugal
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Simões AS, Tavares DA, Rolo D, Ardanuy C, Goossens H, Henriques-Normark B, Linares J, de Lencastre H, Sá-Leão R. lytA-based identification methods can misidentify Streptococcus pneumoniae. Diagn Microbiol Infect Dis 2016; 85:141-8. [PMID: 27107535 DOI: 10.1016/j.diagmicrobio.2016.03.018] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 02/19/2016] [Accepted: 03/20/2016] [Indexed: 02/01/2023]
Abstract
During surveillance studies we detected, among over 1500 presumptive pneumococci, 11 isolates displaying conflicting or novel results when characterized by widely accepted phenotypic (optochin susceptibility and bile solubility) and genotypic (lytA-BsaAI-RFLP and MLST) identification methods. We aimed to determine the genetic basis for the unexpected results given by lytA-BsaAI-RFLP and investigate the accuracy of the WHO recommended lytA real-time PCR assay to classify these 11 isolates. Three novel lytA-BsaAI-RFLP signatures were found (one in pneumococcus and two in S. mitis). In addition, one pneumococcus displayed the atypical lytA-BsaAI-RFLP signature characteristic of non-pneumococci and two S. pseudopneumoniae displayed the typical lytA-BsaAI-RFLP pattern characteristic of pneumococci. lytA real-time PCR misidentified these three isolates. In conclusion, identification of pneumococci by lytA real-time PCR, and other lytA-based methodologies, may lead to false results. This is of particular relevance in the increasingly frequent colonization studies relying solely on culture-independent methods.
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Affiliation(s)
- Alexandra S Simões
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica António Xavier (ITQB), Universidade Nova de Lisboa (UNL), Oeiras, Portugal
| | - Débora A Tavares
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica António Xavier (ITQB), Universidade Nova de Lisboa (UNL), Oeiras, Portugal
| | - Dora Rolo
- Microbiology Department, Hospital Universitari de Bellvitge, Universitat de Barcelona-IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain; CIBERES (Ciber de Enfermedades Respiratorias), ISCIII, Madrid, Spain
| | - Carmen Ardanuy
- Microbiology Department, Hospital Universitari de Bellvitge, Universitat de Barcelona-IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain; CIBERES (Ciber de Enfermedades Respiratorias), ISCIII, Madrid, Spain
| | - Herman Goossens
- Department of Medical Microbiology, University of Antwerp, Antwerp, Belgium; Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Birgitta Henriques-Normark
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden; Department of Laboratory Medicine, Division of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Josefina Linares
- Microbiology Department, Hospital Universitari de Bellvitge, Universitat de Barcelona-IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain; CIBERES (Ciber de Enfermedades Respiratorias), ISCIII, Madrid, Spain
| | - Hermínia de Lencastre
- Laboratory of Molecular Genetics, ITQB, UNL, Oeiras, Portugal; Laboratory of Microbiology and Infectious Diseases, The Rockefeller University, New York, NY, USA
| | - Raquel Sá-Leão
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica António Xavier (ITQB), Universidade Nova de Lisboa (UNL), Oeiras, Portugal.
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Nunes S, Félix S, Valente C, Simões AS, Tavares DA, Almeida ST, Paulo AC, Brito-Avô A, de Lencastre H, Sá-Leão R. The impact of private use of PCV7 in 2009 and 2010 on serotypes and antimicrobial resistance of Streptococcus pneumoniae carried by young children in Portugal: Comparison with data obtained since 1996 generating a 15-year study prior to PCV13 introduction. Vaccine 2016; 34:1648-56. [PMID: 26920470 DOI: 10.1016/j.vaccine.2016.02.045] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 02/11/2016] [Accepted: 02/16/2016] [Indexed: 10/22/2022]
Abstract
In Portugal, the 7-valent pneumococcal conjugate vaccine (PCV7) was not introduced in the national immunization plan but was commercially available between 2001 and 2010. We studied serotype distribution and antibiotic susceptibility of Streptococcus pneumoniae carried by children in 2009 and 2010. Vaccination with PCV7 was extracted from children's immunization bulletins and information on recent antimicrobial consumption was obtained through a questionnaire. For comparison, we included data from previous studies conducted since 1996: 1996-1999, 2001-2003, 2006-2007. Pneumococci were isolated from nasopharyngeal samples of 1092 children up to six years old attending day-care in an urban area. Among these, 76% (819/1070) were vaccinated and 62% (677/1092) carried pneumococci. In 2009-2010, serotype replacement was extensive. Carriage of PCV7 serotypes was 4.9% and 5.8%, in 2009 and 2010, respectively, with the majority being of serotype 19F (carried by 4.3% and 4.6% of all participants, respectively). Colonization by serotype 19F was associated with vaccine status (7.7% (19/248) of non-vaccinees vs. 3.5% (29/818) of PCV7-vaccinees, p=0.010). Carriage of serotype 19A was high in 2009 and 2010 (8.6% of all participants) consistent with values already observed in 2007; carriage of serotype 6A was <1% (10/1092), indicating a major decline after 2007 (5.8% or 31/538, p<0.001). Non-vaccine serotypes increased and serotype 6C became the most frequently carried serotype in 2010 (11.2% (54/481)). High-level resistance to penicillin (MIC ≥2mg/L) showed a decreasing trend (p<0.001), whereas resistance to both penicillin and erythromycin increased (p<0.001) and was detected in 15-20% of all isolates in 2009-2010, most of which were non-vaccine serotypes. Antimicrobial use decreased over time (p<0.001). In conclusion, widespread private use of PCV7 has impacted on colonization leading to near elimination of all PCV7 serotypes except for serotype 19F. Antimicrobial consumption declined but it may be too soon to observe generalized changes in antimicrobial resistance rates.
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Affiliation(s)
- Sónia Nunes
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB/UNL), Oeiras, Portugal; Laboratory of Molecular Genetics, ITQB/UNL, Oeiras, Portugal
| | - Sofia Félix
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB/UNL), Oeiras, Portugal; Laboratory of Molecular Genetics, ITQB/UNL, Oeiras, Portugal
| | - Carina Valente
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB/UNL), Oeiras, Portugal; Laboratory of Molecular Genetics, ITQB/UNL, Oeiras, Portugal
| | - Alexandra S Simões
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB/UNL), Oeiras, Portugal; Laboratory of Molecular Genetics, ITQB/UNL, Oeiras, Portugal
| | - Débora A Tavares
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB/UNL), Oeiras, Portugal; Laboratory of Molecular Genetics, ITQB/UNL, Oeiras, Portugal
| | - Sónia T Almeida
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB/UNL), Oeiras, Portugal; Laboratory of Molecular Genetics, ITQB/UNL, Oeiras, Portugal
| | - Ana C Paulo
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB/UNL), Oeiras, Portugal; Laboratory of Molecular Genetics, ITQB/UNL, Oeiras, Portugal
| | | | - Hermínia de Lencastre
- Laboratory of Molecular Genetics, ITQB/UNL, Oeiras, Portugal; Laboratory of Microbiology and Infectious Diseases, The Rockefeller University, New York, NY, USA
| | - Raquel Sá-Leão
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB/UNL), Oeiras, Portugal; Laboratory of Molecular Genetics, ITQB/UNL, Oeiras, Portugal.
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Gil M, Pinto P, Simões AS, Póvoa P, Da Silva MM, Lapão LV. Co-Design of a Computer-Assisted Medical Decision Support System to Manage Antibiotic Prescription in an ICU Ward. Stud Health Technol Inform 2016; 228:499-503. [PMID: 27577433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
About 37 thousand people die per year in Europe due to infections by resistant bacteria. Fighting antimicrobial resistances (AR) is a top priority to save lives and reduce costs. AR is triggered mostly by uncritical antibiotic prescription. This paper presents HAITool, a decision-making information system to support antibiotic prescription. The system was co-developed together with health professionals using Design Science Research Methodology, empowered with innovative data visualization techniques to improve AR management. HAITool includes integrated visualizations of patient, microbiology, and pharmacy data, facilitating clinical decision support, antibiotic prescriptions quality and antibiotic-resistant bacteria monitoring. It also includes an alert module that monitors conformance of antibiotic prescriptions with norms and guidelines. HAITool is evaluated using both the Österle principles and interviews with physicians and infection control team from three participant hospitals.
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Affiliation(s)
- Miguel Gil
- Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Portugal
| | - Pedro Pinto
- Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Portugal
| | - Alexandra S Simões
- Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Portugal
| | - Pedro Póvoa
- UCIP, Hospital São Francisco Xavier, Centro Hospitalar Lisboa Ocidental, Portugal
| | | | - Luís Velez Lapão
- Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Portugal
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Raddaoui A, Simões AS, Baaboura R, Félix S, Achour W, Ben Othman T, Béjaoui M, Sá-Leão R, Ben Hassen A. Serotype Distribution, Antibiotic Resistance and Clonality of Streptococcus pneumoniae Isolated from Immunocompromised Patients in Tunisia. PLoS One 2015; 10:e0140390. [PMID: 26461259 PMCID: PMC4604151 DOI: 10.1371/journal.pone.0140390] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 09/24/2015] [Indexed: 11/19/2022] Open
Abstract
Background Pneumococcal disease, a major cause of morbidity and mortality globally, has higher incidence among young children, the elderly and the immunocompromised of all ages. In Tunisia, pneumococcal conjugate vaccines (PCVs) are not included in the national immunization program. Also, few studies have described the epidemiology of S. pneumoniae in this country and, in particular, no molecular typing studies have been performed. The aim of this study was to evaluate serotype distribution, antimicrobial resistance and clonality of Streptococcus pneumoniae isolated from neutropenic patients in Tunisia. Methods Fifty-nine S. pneumoniae were isolated from infection (n = 31) and colonization (n = 28) sites of patients (children and adults) attending the National Centre of Bone Marrow Transplantation in Tunis between 2005–2011. All isolates were characterized by serotype, antimicrobial resistance pattern and multilocus sequence typing (MLST). Results The majority (66.1%) of the isolates belonged to five serotypes all included in PCVs: 6B, 9V, 14, 19F and 23F. The potential coverage of the 10-valent and 13-valent PCV was of 71.2% and 76.3% respectively. Resistance rates were very high and 69.5% of the isolates were multidrug resistant: non-susceptibility rates to penicillin, amoxicillin and cefotaxime were 66.1%, 40.7% and 27.1%, respectively; resistance rates to erythromycin, clindamycin, tetracycline, chloramphenicol and trimethoprim-sulfamethoxazole, were 69.5%, 61.0%, 37.3%, 22.0% and 67.8%, respectively. The most frequent serotypes had STs characteristic of multidrug resistant international clones known to be highly successful and important causes of pneumococcal infection: Spain 23F-ST81, France 9V/14-ST156, Spain 6B-ST90, 19F-ST320, and Portugal 19F-ST177. Conclusions The majority of S. pneumoniae strains recovered from immunocompromised patients in Tunisia are representatives of multidrug resistant pandemic clones that express serotypes targeted by PCVs. To contain the burden of pneumococcal disease and improve treatment choices among Tunisian immunocompromised patients PCVs should be offered to all of them.
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Affiliation(s)
- Anis Raddaoui
- Laboratory of the National Bone Marrow Transplantation Centre, Bab Saadoun, Tunis, Tunisie
- University of Carthage, Faculty of Sciences of Bizerte, Tunis, Tunisie
| | - Alexandra S. Simões
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Rekaya Baaboura
- Laboratory of the National Bone Marrow Transplantation Centre, Bab Saadoun, Tunis, Tunisie
- UR12ES02, Microbiologie de la Greffe de Moelle Osseuse, Université Tunis El Manar, 2092, Tunis, Tunisie
| | - Sofia Félix
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Wafa Achour
- Laboratory of the National Bone Marrow Transplantation Centre, Bab Saadoun, Tunis, Tunisie
- UR12ES02, Microbiologie de la Greffe de Moelle Osseuse, Université Tunis El Manar, 2092, Tunis, Tunisie
| | - Tarek Ben Othman
- Hematology Ward, National Bone Marrow Transplantation Centre, Bab Saadoun, Tunis, Tunisie
| | - Mohamed Béjaoui
- Pediatric Immuno-hematology Ward, National Bone Marrow Transplantation Centre, Bab Saadoun, Tunis, Tunisie
| | - Raquel Sá-Leão
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- * E-mail: (ABH); (RSL)
| | - Assia Ben Hassen
- Laboratory of the National Bone Marrow Transplantation Centre, Bab Saadoun, Tunis, Tunisie
- UR12ES02, Microbiologie de la Greffe de Moelle Osseuse, Université Tunis El Manar, 2092, Tunis, Tunisie
- * E-mail: (ABH); (RSL)
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Tavares DA, Simões AS, Bootsma HJ, Hermans PW, de Lencastre H, Sá-Leão R. Non-typeable pneumococci circulating in Portugal are of cps type NCC2 and have genomic features typical of encapsulated isolates. BMC Genomics 2014; 15:863. [PMID: 25283442 PMCID: PMC4200197 DOI: 10.1186/1471-2164-15-863] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Accepted: 09/29/2014] [Indexed: 11/24/2022] Open
Abstract
Background Pneumococcus is a major human pathogen and the polysaccharide capsule is considered its main virulence factor. Nevertheless, strains lacking a capsule, named non-typeable pneumococcus (NT), are maintained in nature and frequently colonise the human nasopharynx. Interest in these strains, not targeted by any of the currently available pneumococcal vaccines, has been rising as they seem to play an important role in the evolution of the species. Currently, there is a paucity of data regarding this group of pneumococci. Also, questions have been raised on whether they are true pneumococci. We aimed to obtain insights in the genetic content of NT and the mechanisms leading to non-typeability and to genetic diversity. Results A collection of 52 NT isolates representative of the lineages circulating in Portugal between 1997 and 2007, as determined by pulsed-field gel electrophoresis and multilocus sequence typing, was analysed. The capsular region was sequenced and comparative genomic hybridisation (CGH) using a microarray covering the genome of 10 pneumococcal strains was carried out. The presence of mobile elements was investigated as source of intraclonal variation. NT circulating in Portugal were found to have similar capsular regions, of cps type NCC2, i.e., having aliB-like ORF1 and aliB-like ORF2 genes. The core genome of NT was essentially similar to that of encapsulated strains. Also, competence genes and most virulence genes were present. The few virulence genes absent in all NT were the capsular genes, type-I and type-II pili, choline-binding protein A (cbpA/pspC), and pneumococcal surface protein A (pspA). Intraclonal variation could not be entirely explained by the presence of prophages and other mobile elements. Conclusions NT circulating in Portugal are a homogeneous group belonging to cps type NCC2. Our observations support the theory that they are bona-fide pneumococcal isolates that do not express the capsule but are otherwise essentially similar to encapsulated pneumococci. Thus we propose that NT should be routinely identified and reported in surveillance studies. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-863) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | - Raquel Sá-Leão
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica (ITQB) António Xavier, Universidade Nova de Lisboa (UNL), Oeiras, Portugal.
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Bajanca-Lavado MP, Simões AS, Betencourt CR, Sá-Leão R. Characteristics of Haemophilus influenzae invasive isolates from Portugal following routine childhood vaccination against H. influenzae serotype b (2002-2010). Eur J Clin Microbiol Infect Dis 2013; 33:603-10. [PMID: 24154654 DOI: 10.1007/s10096-013-1994-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Accepted: 10/03/2013] [Indexed: 10/26/2022]
Abstract
We aimed to characterize Haemophilus influenzae invasive isolates recovered in Portugal over a 9-year period (2002-2010) following the inclusion of H. influenzae serotype b (Hib) conjugate vaccination in the National Immunization Program (NIP) in the year 2000 and compare the results with those obtained in a similar study from the pre-vaccination era (1989-2001) previously described by us. As part of a laboratory-based passive surveillance system, 144 invasive isolates obtained in 28 Portuguese hospitals were received at the National Reference Laboratory for Bacterial Respiratory Infections and were characterized. Capsular types and antibiotic susceptibility patterns were determined. The ftsI gene encoding PBP3 was sequenced for β-lactamase-negative ampicillin-resistant (BLNAR) isolates. Genetic relatedness among isolates was examined by multilocus sequencing typing (MLST). Most isolates (77.1%) were non-capsulated, a significant increase compared to the pre-vaccination era (19.0%, p < 0.001). Serotype b strains decreased significantly (from 81.0 to 13.2%, p < 0.001) and serotype f increased significantly (from 0.8 to 6.9%, p = 0.03). Ten percent of the isolates were β-lactamase producers, a value lower than that previously observed (26.9%, p = 0.005). Eight percent of all isolates were BLNAR. A high genetic diversity among non-capsulated isolates was found. By contrast, capsulated isolates were clonal. The implementation of Hib vaccination has resulted in a significant decline in the proportion of serotype b H. influenzae invasive disease isolates. Most episodes of invasive disease occurring in Portugal are now due to fully susceptible, highly diverse, non-capsulated strains. Given the evolving dynamics of this pathogen and the increase in non-type b capsulated isolates, continuous surveillance is needed.
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Affiliation(s)
- M P Bajanca-Lavado
- National Reference Laboratory for Bacterial Respiratory Infections, Department of Infectious Disease, National Institute of Health Dr. Ricardo Jorge, Av. Padre Cruz, 1649-016, Lisboa, Portugal,
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Rolo D, S. Simões A, Domenech A, Fenoll A, Liñares J, de Lencastre H, Ardanuy C, Sá-Leão R. Disease isolates of Streptococcus pseudopneumoniae and non-typeable S. pneumoniae presumptively identified as atypical S. pneumoniae in Spain. PLoS One 2013; 8:e57047. [PMID: 23437306 PMCID: PMC3578818 DOI: 10.1371/journal.pone.0057047] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Accepted: 01/16/2013] [Indexed: 11/27/2022] Open
Abstract
We aimed to obtain insights on the nature of a collection of isolates presumptively identified as atypical Streptococcus pneumoniae recovered from invasive and non-invasive infections in Spain. One-hundred and thirty-two isolates were characterized by: optochin susceptibility in ambient and CO2-enriched atmosphere; bile solubility; PCR-based assays targeting pneumococcal genes lytA, ply, pspA, cpsA, Spn9802, aliB-like ORF2, and a specific 16S rRNA region; multilocus sequence analysis; and antimicrobial susceptibility. By multilocus sequence analysis, 61 isolates were S. pseudopneumoniae, 34 were pneumococci, 13 were S. mitis, and 24 remained unclassified as non-pneumococci. Among S. pseudopneumoniae isolates, 51 (83.6%) were collected from respiratory tract samples; eight isolates were obtained from sterile sources. High frequency of non-susceptibility to penicillin (60.7%) and erythromycin (42.6%) was found. Only 50.8% of the S. pseudopneumoniae isolates displayed the typical optochin phenotype originally described for this species. None harbored the cpsA gene or the pneumococcal typical lytA restriction fragment length polymorphism. The Spn9802 and the specific 16S rRNA regions were detected among the majority of the S. pseudopneumoniae isolates (n = 59 and n = 49, respectively). The ply and pspA genes were rarely found. A high genetic diversity was found and 59 profiles were identified. Among the S. pneumoniae, 23 were capsulated and 11 were non-typeable. Three non-typeable isolates, associated to international non-capsulated lineages, were recovered from invasive disease sources. In conclusion, half of the atypical pneumococcal clinical isolates were, in fact, S. pseudopneumoniae and one-fourth were other streptococci. We identified S. pseudopneumoniae and non-typeable pneumococci as cause of disease in Spain including invasive disease.
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Affiliation(s)
- Dora Rolo
- Institut d'Investigació Biomèdica de Bellvitge, Hospital Universitari de Bellvitge, Microbiology Department, Universistat de Barcelona, Barcelona, Spain
- Centro de investigación en red de enfermedades respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Alexandra S. Simões
- Laboratory of Molecular Genetics, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Arnau Domenech
- Institut d'Investigació Biomèdica de Bellvitge, Hospital Universitari de Bellvitge, Microbiology Department, Universistat de Barcelona, Barcelona, Spain
- Centro de investigación en red de enfermedades respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Asunción Fenoll
- National Center for Microbiology, Instituto de Salud Carlos III, Madrid, Spain
| | - Josefina Liñares
- Institut d'Investigació Biomèdica de Bellvitge, Hospital Universitari de Bellvitge, Microbiology Department, Universistat de Barcelona, Barcelona, Spain
- Centro de investigación en red de enfermedades respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Hermínia de Lencastre
- Laboratory of Molecular Genetics, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
- Laboratory of Microbiology, The Rockefeller University, New York, New York, United States of America
| | - Carmen Ardanuy
- Institut d'Investigació Biomèdica de Bellvitge, Hospital Universitari de Bellvitge, Microbiology Department, Universistat de Barcelona, Barcelona, Spain
- Centro de investigación en red de enfermedades respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Raquel Sá-Leão
- Laboratory of Molecular Genetics, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
- * E-mail:
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Simões AS, Valente C, de Lencastre H, Sá-Leão R. Rapid identification of noncapsulated Streptococcus pneumoniae in nasopharyngeal samples allowing detection of co-colonization and reevaluation of prevalence. Diagn Microbiol Infect Dis 2011; 71:208-16. [DOI: 10.1016/j.diagmicrobio.2011.07.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2011] [Revised: 07/05/2011] [Accepted: 07/25/2011] [Indexed: 10/17/2022]
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Sá-Leão R, Nunes S, Brito-Avô A, Frazão N, Simões AS, Crisóstomo MI, Paulo ACS, Saldanha J, Santos-Sanches I, de Lencastre H. Changes in pneumococcal serotypes and antibiotypes carried by vaccinated and unvaccinated day-care centre attendees in Portugal, a country with widespread use of the seven-valent pneumococcal conjugate vaccine. Clin Microbiol Infect 2009; 15:1002-7. [PMID: 19392883 DOI: 10.1111/j.1469-0691.2009.02775.x] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The seven-valent pneumococcal conjugate vaccine (PCV7) has been available in Portugal since June 2001, but is not included in the National Vaccination Plan. Its impact on colonization is unknown. A point-prevalence study to evaluate PCV7 usage was carried out in 2006 among day-care centre attendees from the Lisbon area. Pneumococcal carriage rates, serotypes, and antibiotypes were determined and compared with results from a similar study conducted in 2001 before vaccine approval. In 2001 and 2006, 717 and 571 children, respectively, were enrolled. In 2006, 45.9% of the participants were appropriately vaccinated and 11.5% were incompletely vaccinated. Carriage of pneumococci remained stable (64.9% in 2001; 68.7% in 2006). Vaccine types (VT) decreased from 53.1% of all pneumococci to 11.2% (p <0.001). Serotype replacement was observed among vaccinated and unvaccinated children. Non-vaccine types (NVT) 1, 6C, 7F, 15A, 16F, 21, 23A, 29, and non-typeable (NT) strains increased significantly; serotype 19A increased, but not significantly. Rates of resistance to penicillin, erythromycin, clindamycin and tetracycline remained stable (p >0.05) due to significant increases in intermediate resistance to penicillin (from 5.5% to 17.8%), erythromycin (from 9.2% to 21.8%), clindamycin (from 6.4% to 19.3%) and tetracycline (from 8.3% to 15.8%) among NVT. Whereas in 2001 resistance among NVT was mostly associated with serotype 19A and NT strains, in 2006 resistance was also found among serotypes 6C, 15A, 24F and 33F. In conclusion, dramatic shifts in serotypes of colonizing pneumococci were observed among vaccinated and unvaccinated children. Rates of antibiotic resistance remained unchanged due to a balance between reduction in VT and an increase in antimicrobial-resistant NVT.
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Affiliation(s)
- R Sá-Leão
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal.
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Sá-Leão R, Simões AS, Nunes S, Sousa NG, Frazão N, de Lencastre H. Identification, prevalence and population structure of non-typable Streptococcus pneumoniae in carriage samples isolated from preschoolers attending day-care centres. Microbiology (Reading) 2006; 152:367-376. [PMID: 16436425 DOI: 10.1099/mic.0.28596-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The authors aimed to get insights into the population structure of non-(sero)typable pneumococci (NTPn), a specific group of natural atypical pneumococci whose identification is often difficult, and which has remained insufficiently studied. A total of 265 presumptive NTPn, isolated between 1997 and 2003 from the nasopharynx of children, were characterized. Strains were confirmed to be pneumococci on the basis of bile solubility, and PCR detection or Southern blotting hybridization of lytA and psaA, genes ubiquitous in this species. Multilocus sequence typing (MLST) was used to exclude two isolates that gave ambiguous results. Non-typability was confirmed by the Quellung reaction using Omniserum. A total of 213 isolates were considered to be true NTPn. The molecular analysis of the true NTPn by PFGE and MLST showed that this population was genetically diverse, although a dominant cluster, accounting for 66 % of the isolates, was identified. Antimicrobial resistance was observed in most genetic backgrounds, and multidrug resistance to penicillin, erythromycin, clindamycin, tetracycline and sulfamethoxazole-trimethoprim was associated with strains belonging to the dominant cluster. Comparison with PFGE fingerprints and sequence types of large collections of serotypable strains showed that the genetic backgrounds of all but two NTPn were different from those found in serotypable strains. In addition, we found that NTPn strains with similar genetic backgrounds to those identified in our study had been isolated from disease sources in other countries. These observations seem to indicate that NTPn have diverse genetic backgrounds and may have evolved as a distinct group of pneumococcal isolates.
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Affiliation(s)
- Raquel Sá-Leão
- Molecular Genetics Laboratory, Instituto de Tecnologia Química e Biológica da Universidade Nova de Lisboa, Rua da Quinta Grande, 6, 2780-106 Oeiras, Portugal
| | - Alexandra S Simões
- Molecular Genetics Laboratory, Instituto de Tecnologia Química e Biológica da Universidade Nova de Lisboa, Rua da Quinta Grande, 6, 2780-106 Oeiras, Portugal
| | - Sónia Nunes
- Molecular Genetics Laboratory, Instituto de Tecnologia Química e Biológica da Universidade Nova de Lisboa, Rua da Quinta Grande, 6, 2780-106 Oeiras, Portugal
| | - Natacha G Sousa
- Molecular Genetics Laboratory, Instituto de Tecnologia Química e Biológica da Universidade Nova de Lisboa, Rua da Quinta Grande, 6, 2780-106 Oeiras, Portugal
| | - Nelson Frazão
- Molecular Genetics Laboratory, Instituto de Tecnologia Química e Biológica da Universidade Nova de Lisboa, Rua da Quinta Grande, 6, 2780-106 Oeiras, Portugal
| | - Hermínia de Lencastre
- Laboratory of Microbiology, The Rockefeller University, NY, USA
- Molecular Genetics Laboratory, Instituto de Tecnologia Química e Biológica da Universidade Nova de Lisboa, Rua da Quinta Grande, 6, 2780-106 Oeiras, Portugal
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Medeiros JT, Simões AS. Heuristic model for the energy spectrum of phase turbulence. Phys Rev E Stat Nonlin Soft Matter Phys 2001; 64:057301. [PMID: 11736148 DOI: 10.1103/physreve.64.057301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2001] [Indexed: 05/23/2023]
Abstract
We present a heuristic model for the energy spectrum of the one-dimensional phase turbulence in the steady state of the Kuramoto-Sivashinsky equation. Our model contains an energy transfer mechanism from low- to high-wave-vector modes. The energy transfer is written as the sum of local and nonlocal interactions. Our analytical results show good agreement with numerical simulations, particularly for the hump in the energy spectrum, which is mainly due to the local interactions.
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Affiliation(s)
- J T Medeiros
- Instituto de Física, Universidade Federal do Rio Grande do Sul, 91501-970 Porto Alegre, RS, Brazil
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