Repository logo

Browsing by Author "Aanensen, David M."

Now showing 1 - 4 of 4
  • Epidemic of carbapenem-resistant Klebsiella pneumoniae in Europe is driven by nosocomial spread
    Publication . David, Sophia; Reuter, Sandra; Harris, Simon R.; Glasner, Corinna; Feltwell, Theresa; Argimon, Silvia; Abudahab, Khalil; Goater, Richard; Giani, Tommaso; Errico, Giulia; Aspbury, Marianne; Sjunnebo, Sara; EuSCAPE Working Group; ESGEM Study Group; Feil, Edward J.; Rossolini, Gian Maria; Aanensen, David M.; Grundmann, Hajo
    Public health interventions to control the current epidemic of carbapenem-resistant Klebsiella pneumoniae rely on a comprehensive understanding of its emergence and spread over a wide range of geographical scales. We analysed the genome sequences and epidemiological data of >1,700 K. pneumoniae samples isolated from patients in 244 hospitals in 32 countries during the European Survey of Carbapenemase-Producing Enterobacteriaceae. We demonstrate that carbapenemase acquisition is the main cause of carbapenem resistance and that it occurred across diverse phylogenetic backgrounds. However, 477 of 682 (69.9%) carbapenemase-positive isolates are concentrated in four clonal lineages, sequence types 11, 15, 101, 258/512 and their derivatives. Combined analysis of the genetic and geographic distances between isolates with different β-lactam resistance determinants suggests that the propensity of K. pneumoniae to spread in hospital environments correlates with the degree of resistance and that carbapenemase-positive isolates have the highest transmissibility. Indeed, we found that over half of the hospitals that contributed carbapenemase-positive isolates probably experienced within-hospital transmission, and interhospital spread is far more frequent within, rather than between, countries. Finally, we propose a value of 21 for the number of single nucleotide polymorphisms that optimizes the discrimination of hospital clusters and detail the international spread of the successful epidemic lineage, ST258/512.
    2019-11Journal article Restricted access Show more
  • Europe-wide expansion and eradication of multidrug-resistant Neisseria gonorrhoeae lineages: a genomic surveillance study
    Publication . Sánchez-Busó, Leonor; Cole, Michelle J.; Spiteri, Gianfranco; Day, Michaela; Jacobsson, Susanne; Golparian, Daniel; Sajedi, Noshin; Yeats, Corin A.; Abudahab, Khalil; Underwood, Anthony; Bluemel, Benjamin; Aanensen, David M.; Unemo, Magnus; Pleininger, Sonja; Indra, Alexander; De Baetselier, Irith; Vanden Berghe, Wim; Hunjak, Blaženka; Blažić, Tatjana Nemeth; Maikanti-Charalambous, Panayiota; Pieridou, Despo; Zákoucká, Hana; Žemličková, Helena; Hoffmann, Steen; Cowan, Susan; Schwartz, Lasse Jessen; Peetso, Rita; Epstein, Jevgenia; Viktorova, Jelena; Ndeikoundam, Ndeindo; Bercot, Beatrice; Bébéar, Cécile; Lot, Florence; Buder, Susanne; Jansen, Klaus; Miriagou, Vivi; Rigakos, Georgios; Raftopoulos, Vasilios; Balla, Eszter; Dudás, Mária; Ásmundsdóttir, Lena Rós; Sigmundsdóttir, Guðrún; Hauksdóttir, Guðrún Svanborg; Gudnason, Thorolfur; Colgan, Aoife; Crowley, Brendan; Saab, Sinéad; Stefanelli, Paola; Carannante, Anna; Parodi, Patrizia; Pakarna, Gatis; Nikiforova, Raina; Bormane, Antra; Dimina, Elina; Perrin, Monique; Abdelrahman, Tamir; Mossong, Joël; Schmit, Jean-Claude; Mühlschlegel, Friedrich; Barbara, Christopher; Mifsud, Francesca; Van Dam, Alje; Van Benthem, Birgit; Visser, Maartje; Linde, Ineke; Kløvstad, Hilde; Caugant, Dominique; Młynarczyk-Bonikowska, Beata; Azevedo, Jacinta; Borrego, Maria-José; Nascimento, Marina Lurdes Ramos; Pavlik, Peter; Klavs, Irena; Murnik, Andreja; Jeverica, Samo; Kustec, Tanja; Vázquez Moreno, Julio; Diaz, Asuncion; Abad, Raquel; Velicko, Inga; Unemo, Magnus; Fifer, Helen; Shepherd, Jill; Patterson, Lynsey
    Background: Genomic surveillance using quality-assured whole-genome sequencing (WGS) together with epidemiological and antimicrobial resistance (AMR) data is essential to characterise the circulating Neisseria gonorrhoeae lineages and their association to patient groups (defined by demographic and epidemiological factors). In 2013, the European gonococcal population was characterised genomically for the first time. We describe the European gonococcal population in 2018 and identify emerging or vanishing lineages associated with AMR and epidemiological characteristics of patients, to elucidate recent changes in AMR and gonorrhoea epidemiology in Europe. Methods: We did WGS on 2375 gonococcal isolates from 2018 (mainly Sept 1-Nov 30) in 26 EU and EEA countries. Molecular typing and AMR determinants were extracted from quality-checked genomic data. Association analyses identified links between genomic lineages, AMR, and epidemiological data. Findings: Azithromycin-resistant N gonorrhoeae (8·0% [191/2375] in 2018) is rising in Europe due to the introduction or emergence and subsequent expansion of a novel N gonorrhoeae multi-antigen sequence typing (NG-MAST) genogroup, G12302 (132 [5·6%] of 2375; N gonorrhoeae sequence typing for antimicrobial resistance [NG-STAR] clonal complex [CC]168/63), carrying a mosaic mtrR promoter and mtrD sequence and found in 24 countries in 2018. CC63 was associated with pharyngeal infections in men who have sex with men. Susceptibility to ceftriaxone and cefixime is increasing, as the resistance-associated lineage, NG-MAST G1407 (51 [2·1%] of 2375), is progressively vanishing since 2009-10. Interpretation: Enhanced gonococcal AMR surveillance is imperative worldwide. WGS, linked to epidemiological and AMR data, is essential to elucidate the dynamics in gonorrhoea epidemiology and gonococcal populations as well as to predict AMR. When feasible, WGS should supplement the national and international AMR surveillance programmes to elucidate AMR changes over time. In the EU and EEA, increasing low-level azithromycin resistance could threaten the recommended ceftriaxone-azithromycin dual therapy, and an evidence-based clinical azithromycin resistance breakpoint is needed. Nevertheless, increasing ceftriaxone susceptibility, declining cefixime resistance, and absence of known resistance mutations for new treatments (zoliflodacin, gepotidacin) are promising.
    2022-06Journal article Open access Show more
  • Occurrence of carbapenemase-producing Klebsiella pneumoniae and Escherichia coli in the European survey of carbapenemase-producing Enterobacteriaceae (EuSCAPE): a prospective, multinational study
    Publication . Grundmann, Hajo; Glasner, Corinna; Albiger, Barbara; Aanensen, David M.; Tomlinson, Chris T.; Andrasević, Arjana Tambić; Cantón, Rafael; Carmeli, Yehuda; Friedrich, Alexander W.; Giske, Christian G.; Glupczynski, Youri; Gniadkowski, Marek; Livermore, David M.; Nordmann, Patrice; Poirel, Laurent; Rossolini, Gian M.; Seifert, Harald; Vatopoulos, Alkiviadis; Walsh, Timothy; Woodford, Neil; Monnet, Dominique L.; EuSCAPE Working Group; Koraqi, A..; Lacej, D.; Apfalter, P.; Hartl, R.; Glupczynski, Y.; Huang, T.D.; Strateva, T; Marteva-Proevska, Y.; Tambic, Andrasevic A.; Butic, I.; Pieridou-Bagatzouni, D.; Maikanti-Charalampous, P.; Hrabak, J.; Zemlickova, H.; Hammerum, A.; Jakobsen, L.; Ivanova, M.; Pavelkovich, A.; Jalava, J.; Österblad, M.; Dortet, L.; Vaux, S.; Kaase, M.; Gatermann, S.G.; Vatopoulos, A.; Tryfinopoulou, K.; Tóth, A.; Jánvári, L.; Boo, T.W.; McGrath, E.; Carmeli, Y.; Adler, A.; Pantosti, A.; Monaco, M.; Raka, L.; Kurti, A.; Balode, A.; Saule, M.; Miciuleviciene, J.; Mierauskaite, A.; Perrin -Weniger, M.; Reichert, P.; Nestorova, N.; Debattista, S.; Mijovic, G.; Lopicic, M.; Samuelsen, Ø.; Haldorsen, B.J.; Żabicka, D.; Literacka, E.; Caniça, M.; Manageiro, V.; Kaftandzieva, A.; Trajkovska-Dokic, E.; Damian, M.; Lixandru, B.; Jelesic, Z.; Trudic, A.; Niks, M.; Schreterova, E.; Pirs, M.; Cerar, T.; Oteo, J.; Aracil, B.; Giske, C.; Sjöström, K.; Gür, D.; Cakar, A.; Woodford, N.; Hopkins, K.; Wiuff, C.; Brown, D.J.
    BACKGROUND: Gaps in the diagnostic capacity and heterogeneity of national surveillance and reporting standards in Europe make it difficult to contain carbapenemase-producing Enterobacteriaceae. We report the development of a consistent sampling framework and the results of the first structured survey on the occurrence of carbapenemase-producing Klebsiella pneumoniae and Escherichia coli in European hospitals. METHODS: National expert laboratories recruited hospitals with diagnostic capacities, who collected the first ten carbapenem non-susceptible clinical isolates of K pneumoniae or E coli and ten susceptible same-species comparator isolates and pertinent patient and hospital information. Isolates and data were relayed back to national expert laboratories, which made laboratory-substantiated information available for central analysis. FINDINGS: Between Nov 1, 2013, and April 30, 2014, 455 sentinel hospitals in 36 countries submitted 2703 clinical isolates (2301 [85%] K pneumoniae and 402 (15%) E coli). 850 (37%) of 2301 K pneumoniae samples and 77 (19%) of 402 E coli samples were carbapenemase (KPC, NDM, OXA-48-like, or VIM) producers. The ratio of K pneumoniae to E coli was 11:1. 1·3 patients per 10 000 hospital admissions had positive clinical specimens. Prevalence differed greatly, with the highest rates in Mediterranean and Balkan countries. Carbapenemase-producing K pneumoniae isolates showed high resistance to last-line antibiotics. INTERPRETATION: This initiative shows an encouraging commitment by all participants, and suggests that challenges in the establishment of a continent-wide enhanced sentinel surveillance for carbapenemase-producing Enterobacteriaeceae can be overcome. Strengthening infection control efforts in hospitals is crucial for controlling spread through local and national health care networks.
    2017-02Journal article Restricted access Show more
  • Public health surveillance of multidrug-resistant clones of Neisseria gonorrhoeae in Europe: a genomic survey
    Publication . Harris, Simon R.; Cole, Michelle J.; Spiteri, Gianfranco; Sánchez-Busó, Leonor; Golparian, Daniel; Jacobsson, Susanne; Goater, Richard; Abudahab, Khalil; Yeats, Corin A.; Bercot, Beatrice; Borrego, Maria José; Crowley, Brendan; Stefanelli, Paola; Tripodo, Francesco; Abad, Raquel; Aanensen, David M.; Unemo, Magnus; Euro-GASP study group
    Background: Traditional methods for molecular epidemiology of Neisseria gonorrhoeae are suboptimal. Whole-genome sequencing (WGS) offers ideal resolution to describe population dynamics and to predict and infer transmission of antimicrobial resistance, and can enhance infection control through linkage with epidemiological data. We used WGS, in conjunction with linked epidemiological and phenotypic data, to describe the gonococcal population in 20 European countries. We aimed to detail changes in phenotypic antimicrobial resistance levels (and the reasons for these changes) and strain distribution (with a focus on antimicrobial resistance strains in risk groups), and to predict antimicrobial resistance from WGS data. Methods: We carried out an observational study, in which we sequenced isolates taken from patients with gonorrhoea from the European Gonococcal Antimicrobial Surveillance Programme in 20 countries from September to November, 2013. We also developed a web platform that we used for automated antimicrobial resistance prediction, molecular typing (N gonorrhoeae multi-antigen sequence typing [NG-MAST] and multilocus sequence typing), and phylogenetic clustering in conjunction with epidemiological and phenotypic data. Findings: The multidrug-resistant NG-MAST genogroup G1407 was predominant and accounted for the most cephalosporin resistance, but the prevalence of this genogroup decreased from 248 (23%) of 1066 isolates in a previous study from 2009–10 to 174 (17%) of 1054 isolates in this survey in 2013. This genogroup previously showed an association with men who have sex with men, but changed to an association with heterosexual people (odds ratio=4·29). WGS provided substantially improved resolution and accuracy over NG-MAST and multilocus sequence typing, predicted antimicrobial resistance relatively well, and identified discrepant isolates, mixed infections or contaminants, and multidrug-resistant clades linked to risk groups. Interpretation: To our knowledge, we provide the first use of joint analysis of WGS and epidemiological data in an international programme for regional surveillance of sexually transmitted infections. WGS provided enhanced understanding of the distribution of antimicrobial resistance clones, including replacement with clones that were more susceptible to antimicrobials, in several risk groups nationally and regionally. We provide a framework for genomic surveillance of gonococci through standardised sampling, use of WGS, and a shared information architecture for interpretation and dissemination by use of open access software.
    2018-07Journal article Restricted access Show more