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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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Nobre C, Moniz P, Faria NA. Methicilin-susceptible Staphylococcus aureus clonal complex 398: An unusual agent of necrotizing pneumonia. Pulmonology 2023:S2531-0437(23)00196-4. [PMID: 38001008 DOI: 10.1016/j.pulmoe.2023.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 10/17/2023] [Accepted: 10/18/2023] [Indexed: 11/26/2023] Open
Affiliation(s)
- C Nobre
- Department of Intensive Care (ICU4), Hospital de São Francisco Xavier Centro Hospitalar Lisboa Ocidental, Estrada do Forte do Alto Duque, 1449-0054 Lisbon, Portugal.
| | - P Moniz
- Department of Intensive Care (ICU4), Hospital de São Francisco Xavier Centro Hospitalar Lisboa Ocidental, Estrada do Forte do Alto Duque, 1449-0054 Lisbon, Portugal
| | - N A Faria
- Laboratory of Bacterial Evolution and Molecular Epidemiology, Instituto de Tecnologia Química e Biológica António Xavier (ITQB-NOVA), Universidade Nova de Lisboa, Avenida da República, 2780-157 Oeiras, Portugal; Laboratory of Molecular Genetics, Instituto de Tecnologia Química e Biológica António Xavier (ITQB-NOVA), Universidade Nova de Lisboa, Avenida da República, 2780-157 Oeiras, Portugal
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Simões AS, Touret T, Faria NA, Peres Ladeiro S, Costa J, Bispo S, Serrano M, Palos C, Miragaia M, Bastos Leite R, Sá-Leão R. Using Whole Genome Sequencing to Investigate a Mock-Outbreak of Carbapenem-Resistant Klebsiella pneumoniae in Real-Time. ACTA MEDICA PORT 2022; 35:36-41. [PMID: 34755594 DOI: 10.20344/amp.15174] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 03/16/2021] [Accepted: 03/29/2021] [Indexed: 11/20/2022]
Abstract
INTRODUCTION Healthcare associated infections due to carbapenem-resistant Klebsiella pneumoniae (CRKP) are a major concern in Portuguese hospitals. Whole genome sequencing (WGS) can improve infection control, but this practice is not routinely used by hospital clinical laboratories in Portugal. We simulated the investigation of a CRKP outbreak based on WGS, with the aim of determining, in the minimum possible time, genetic relatedness between CRKP clinical and environmental isolates. MATERIAL AND METHODS Ten CRKP clinical isolates routinely obtained in the hospital laboratory were used. Forty environmental samples - from sinks and sink drains of ward rooms - were collected. Environmental samples were plated on selective media and presumptive CRKP colonies were isolated. Total DNA was extracted from all putative CRKP isolates and sequenced. Clonal relatedness was determined by multi-locus sequence typing and core genome single nucleotide polymorphism analysis; the presence of carbapenemase genes was evaluated. RESULTS Clinical isolates were characterized in 48 hours: eight strains were confirmed as CRKP, of which six were of ST13 and carried blaKPC-3. Environmental samples results were obtained in six days: eight CRKP were isolated from which five were of ST13 and carried blaKPC-3. Clinical and environmental ST13 isolates were highly related: ten (of 11) isolates differed from each other in < 0.001% of 2 172 367 core nucleotides. DISCUSSION WGS can be used as a high-resolution effective tool to investigate healthcare associated infections and track routes of dissemination in real-time. CONCLUSION In Portugal, routine use of WGS to improve infection control could thrive through collaborative initiatives between hospitals and research institutes.
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Affiliation(s)
- Alexandra Sofia Simões
- Laboratory of Molecular Microbiology of Human Pathogens. Instituto de Tecnologia Química e Biológica António Xavier. Universidade Nova de Lisboa. Oeiras. Portugal
| | - Tiago Touret
- Laboratory of Molecular Microbiology of Human Pathogens. Instituto de Tecnologia Química e Biológica António Xavier. Universidade Nova de Lisboa. Oeiras. Portugal
| | - Nuno Alexandre Faria
- Laboratory of Bacterial Evolution and Molecular Epidemiology. Instituto de Tecnologia Química e Biológica António Xavier. Universidade Nova de Lisboa. Oeiras. Portugal
| | | | - João Costa
- Unidade de Genoma. Instituto Gulbenkian da Ciência. Oeiras. Portugal
| | - Soraia Bispo
- Grupo Coordenador Local do Programa de Prevenção e Controlo de Infeções e de Resistência aos Antimicrobianos. Hospital Beatriz Ângelo. Loures. Portugal
| | - Mónica Serrano
- Laboratory of Microbial Development. Instituto de Tecnologia Química e Biológica António Xavier. Universidade Nova de Lisboa. Oeiras. Portugal
| | - Carlos Palos
- Grupo Coordenador Local do Programa de Prevenção e Controlo de Infeções e de Resistência aos Antimicrobianos. Hospital Beatriz Ângelo. Loures. Portugal
| | - Maria Miragaia
- Laboratory of Bacterial Evolution and Molecular Epidemiology. Instituto de Tecnologia Química e Biológica António Xavier. Universidade Nova de Lisboa. Oeiras. Portugal
| | | | - Raquel Sá-Leão
- Laboratory of Molecular Microbiology of Human Pathogens. Instituto de Tecnologia Química e Biológica António Xavier. Universidade Nova de Lisboa. Oeiras. Portugal
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Deplano A, Dodémont M, Denis O, Westh H, Gumpert H, Larsen AR, Larsen J, Kearns A, Pichon B, Layer F, Schulte B, Wolz C, Spiliopoulou I, Brennan G, Empel J, Hryniewicz W, de Lencastre H, Faria NA, Codita I, Sabat AJ, Friedrich AW, Deurenberg RH, Tristan A, Laurent F, Vandenesch F. European external quality assessments for identification, molecular typing and characterization of Staphylococcus aureus. J Antimicrob Chemother 2019; 73:2662-2666. [PMID: 30099486 DOI: 10.1093/jac/dky260] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 06/07/2018] [Indexed: 11/13/2022] Open
Abstract
Objectives We present the results of two European external quality assessments (EQAs) conducted in 2014 and 2016 under the auspices of the Study Group on Staphylococci and Staphylococcal Infections of ESCMID. The objective was to assess the performance of participating centres in characterizing Staphylococcus aureus using their standard in-house phenotypic and genotypic protocols. Methods A total of 11 well-characterized blindly coded S. aureus (n = 9), Staphylococcus argenteus (n = 1) and Staphylococcus capitis (n = 1) strains were distributed to participants for analysis. Species identification, MIC determination, antimicrobial susceptibility testing, antimicrobial resistance and toxin gene detection and molecular typing including spa typing, SCCmec typing and MLST were performed. Results Thirteen laboratories from 12 European countries participated in one EQA or both EQAs. Despite considerable diversity in the methods employed, good concordance (90%-100%) with expected results was obtained. Discrepancies were observed for: (i) identification of the S. argenteus strain; (ii) phenotypic detection of low-level resistance to oxacillin in the mecC-positive strain; (iii) phenotypic detection of the inducible MLSB strain; and (iv) WGS-based detection of some resistance and toxin genes. Conclusions Overall, good concordance (90%-100%) with expected results was observed. In some instances, the accurate detection of resistance and toxin genes from WGS data proved problematic, highlighting the need for validated and internationally agreed-on bioinformatics pipelines before such techniques are implemented routinely by microbiology laboratories. We strongly recommend all national reference laboratories and laboratories acting as referral centres to participate in such EQA initiatives.
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Affiliation(s)
- Ariane Deplano
- Centre National de Référence S. aureus, Hôpital Erasme - Université Libre de Bruxelles (ULB), 808 Route de Lennik, Bruxelles, Belgium
| | - Magali Dodémont
- Centre National de Référence S. aureus, Hôpital Erasme - Université Libre de Bruxelles (ULB), 808 Route de Lennik, Bruxelles, Belgium
| | - Olivier Denis
- Centre National de Référence S. aureus, Hôpital Erasme - Université Libre de Bruxelles (ULB), 808 Route de Lennik, Bruxelles, Belgium
| | - Henrik Westh
- MRSA Knowledge Center, Hvidovre Hospital, Kettegard Alle 30, Hvidrove, Denmark.,Institute of Clinical Medicine, Faculty of Medicine and Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Heidi Gumpert
- MRSA Knowledge Center, Hvidovre Hospital, Kettegard Alle 30, Hvidrove, Denmark
| | - Anders Rhod Larsen
- National Reference Laboratory for Antimicrobial Resistance and Staphylococci, Statens Serum Institut, Artllerivej 5, Copenhagen, Denmark
| | - Jesper Larsen
- National Reference Laboratory for Antimicrobial Resistance and Staphylococci, Statens Serum Institut, Artllerivej 5, Copenhagen, Denmark
| | - Angela Kearns
- Staphylococcus Reference Service, National Infection Service, Public Health England, 61 Colindale Avenue, London, UK
| | - Bruno Pichon
- Staphylococcus Reference Service, National Infection Service, Public Health England, 61 Colindale Avenue, London, UK
| | - Franziska Layer
- Nationale referenzzeebtrum fûr Staphylokokken, Robert Koch Institute, Burgstraße 37, Wernigerode, Germany
| | - Berit Schulte
- Institute für Medizinische Mikrobiologie und Hygiene, Universitätsklinikum Tübingen, Elfriede-Aulhorn-Strasse 6, Tübingen, Germany
| | - Christiane Wolz
- Institute für Medizinische Mikrobiologie und Hygiene, Universitätsklinikum Tübingen, Elfriede-Aulhorn-Strasse 6, Tübingen, Germany
| | - Iris Spiliopoulou
- National Staphylococcal Reference Laboratory, Department of Microbiology, School of Medicine, University of Patras, Rion, Patras, Greece
| | - Gráinne Brennan
- National MRSA Reference Laboratory, St James's Hospital, James's Street, Dublin, Ireland
| | - Joanna Empel
- Department of Epidemiology and Clinical Microbiology, Narodowy Instytut Leków, Chelmska 30/34, Warsaw, Poland
| | - Waleria Hryniewicz
- Department of Epidemiology and Clinical Microbiology, Narodowy Instytut Leków, Chelmska 30/34, Warsaw, Poland
| | - Herminia de Lencastre
- Laboratory of Molecular Genetics, Instituto de Tecnologia Química e Biológica António Xavier (ITQB), Universidade Nova de Lisboa, Av. da República, Oeiras, Portugal.,Laboratory of Microbiology & Infectious Diseases, The Rockefeller University, 1230 York Ave., New York, NY, USA
| | - Nuno Alexandre Faria
- Laboratory of Molecular Genetics, Instituto de Tecnologia Química e Biológica António Xavier (ITQB), Universidade Nova de Lisboa, Av. da República, Oeiras, Portugal.,Bacterial Evolution and Molecular Epidemiology, Instituto de Tecnologia Química e Biológica António Xavier (ITQB), Universidade Nova de Lisboa, Av. da República, Oeiras, Portugal
| | - Irina Codita
- Cantazuno National Institute of Research, Staphylococcus Reference Laboratory, INC Cantacuzino Splaiul Independentei 103, Bucarest, Romania
| | - Artur J Sabat
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Hanzeplein 1, RB Groningen, The Netherlands
| | - Alexander W Friedrich
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Hanzeplein 1, RB Groningen, The Netherlands
| | - Ruud H Deurenberg
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Hanzeplein 1, RB Groningen, The Netherlands
| | - Anne Tristan
- Centre National de Référence des Staphylocoques, Institut des Agents Infectieux, Hospices Civils de Lyon, 103 Grande Rue de la Croix Rousse, Lyon, France
| | - Frédéric Laurent
- Centre National de Référence des Staphylocoques, Institut des Agents Infectieux, Hospices Civils de Lyon, 103 Grande Rue de la Croix Rousse, Lyon, France
| | - François Vandenesch
- Centre National de Référence des Staphylocoques, Institut des Agents Infectieux, Hospices Civils de Lyon, 103 Grande Rue de la Croix Rousse, Lyon, France
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Almeida ST, Nunes S, Paulo ACS, Faria NA, de Lencastre H, Sá-Leão R. Prevalence, risk factors, and epidemiology of methicillin-resistant Staphylococcus aureus carried by adults over 60 years of age. Eur J Clin Microbiol Infect Dis 2014; 34:593-600. [PMID: 25359581 DOI: 10.1007/s10096-014-2267-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2014] [Accepted: 10/15/2014] [Indexed: 11/30/2022]
Abstract
The epidemiology of methicillin-resistant Staphylococcus aureus (MRSA) in the community in Portugal is not completely understood. To evaluate S. aureus and MRSA carriage among the elderly, we conducted a large cross-sectional study between April 2010 and December 2012. A total of 3,361 adults over 60 years of age were screened for S. aureus nasopharyngeal and oropharyngeal carriage. MRSA were characterized by staphylococcal cassette chromosome mec (SCCmec) typing, spa typing, multilocus sequence typing (MLST), and tested for the presence of Panton-Valentine leukocidin (PVL). Risk factors for MRSA carriage were identified by multiple logistic regression analysis. The prevalence of S. aureus and MRSA carriage among the elderly was 20.1 % and 1.8 %, respectively. The risk of being an MRSA carrier was higher among the elderly living in retirement homes [odds ratio (OR) = 2.90, 95 % confidence interval (CI): 1.48-5.48] and those that had been hospitalized in the previous year (OR = 2.64, 95 % CI: 1.47-4.58). Among the 62 MRSA isolates, 64.5 % were multidrug-resistant and none carried PVL. Most MRSA (82.3 %) were related to three hospital-associated (HA-MRSA) clones disseminated in Portugal: ST105-II (New York/Japan clone; 43.5 %), ST5-IVc (Pediatric clone; 19.4 %), and ST22-IVh (EMRSA-15 clone; 19.4 %). The New York/Japan and Pediatric clones were significantly associated with carriers living in retirement homes, while the EMRSA-15 clone was associated with carriers that had been hospitalized. We conclude that the elderly population in Portugal is essentially free of MRSA. Given the current European societal challenges for a healthy active aging, these results are of importance to healthcare professionals and public authorities to decide on strategies to promote health in this age group.
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Affiliation(s)
- S T Almeida
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica António Xavier (ITQB), Universidade Nova de Lisboa (UNL), Av. da República, 2780-157, Oeiras, Portugal
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Amorim ML, Faria NA, Oliveira DC, Vasconcelos C, Cabeda JC, Mendes AC, Calado E, Castro AP, Ramos MH, Amorim JM, de Lencastre H. Changes in the clonal nature and antibiotic resistance profiles of methicillin-resistant Staphylococcus aureus isolates associated with spread of the EMRSA-15 clone in a tertiary care Portuguese hospital. J Clin Microbiol 2007; 45:2881-8. [PMID: 17626175 PMCID: PMC2045296 DOI: 10.1128/jcm.00603-07] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Two hundred eighty methicillin-resistant Staphylococcus aureus (MRSA) clinical isolates recovered from a tertiary care hospital in Oporto, Portugal, between 2003 and 2005 were studied by a combination of molecular typing techniques in order to investigate the genetic backgrounds associated with the changes in the resistance phenotypes observed since 2001 and compare them to those previously found in the hospital. All MRSA isolates were grouped into resistance profiles for a panel of seven antibiotics and characterized by pulsed-field gel electrophoresis (PFGE) and SCCmec (staphylococcal cassette chromosome mec) typing. Representative isolates of PFGE types were further studied by spa typing and multilocus sequence typing. Our findings clearly document that the increasing isolation of nonmultiresistant MRSA strains was associated with the decline (from 69% in 1996 to 2000 to 12% in 2003 to 2005) and massive replacement of the multiresistant Brazilian clone (ST239-IIIA) by the epidemic EMRSA-15 clone (ST22-IV), in which resistance to antibiotics other than beta-lactams is very rare, as the major clone (80% of isolates). The Iberian clone (ST247-IA), a major clone in 1992 to 1993, was represented in the present study by just one isolate. Two other pandemic MRSA clones were detected, as sporadic isolates, for the first time in our hospital: the New York/Japan (ST5-II) and the EMRSA-16 (ST36-II) clones. Furthermore, the pattern of susceptibility of MRSA isolates both to gentamicin and to trimethoprim-sulfamethoxazole was shown to be an excellent phenotypic marker for the discrimination of the EMRSA-15 clone from other nonmultiresistant MRSA clones present in our hospital.
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Affiliation(s)
- M L Amorim
- Laboratório de Genética Molecular, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa (ITQB/UNL), Oeiras, Portugal
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