Editorial team Editorial advisors Based at the European Centre for Albania: Alban Ylli, Tirana Disease Prevention and Control (ECDC), Austria: Reinhild Strauss, Vienna 171 83 Stockholm, Sweden Belgium: Koen De Schrijver, Antwerp Telephone number Belgium: Sophie Quoilin, Brussels +46 (0)8 58 60 11 38 or +46 (0)8 58 60 11 36 Bosnia and Herzogovina: Nina Rodić Vukmir, Banja Luka Fax number Bulgaria: Mira Kojouharova, Sofia +46 (0)8 58 60 12 94 Croatia: TBC, Zagreb Cyprus: Chrystalla Hadjianastassiou, Nicosia E-mail Czech Republic: Bohumir Križ, Prague [email protected] Denmark: Peter Henrik Andersen, Copenhagen Editor-in-chief England and Wales: TBC, London Ines Steffens Estonia: Kuulo Kutsar, Tallinn Finland: Outi Lyytikäinen, Helsinki Scientific editors France: Judith Benrekassa, Paris Kathrin Hagmaier Germany: Jamela Seedat, Berlin Williamina Wilson Greece: Rengina Vorou, Athens Karen Wilson Hungary: Ágnes Csohán, Budapest Assistant editors Iceland: Haraldur Briem, Reykjavik Alina Buzdugan Ireland: Lelia Thornton, Dublin Ingela Söderlund Italy: Paola De Castro, Rome Associate editors Kosovo (under UNSCR 1244/99): Lul Raka, Pristina Andrea Ammon, Stockholm, Sweden Latvia: Jurijs Perevoščikovs, Riga Tommi Asikainen, Frankfurt, Germany Lithuania: Milda Zygutiene, Vilnius Mike Catchpole, London, United Kingdom Luxembourg: Thérèse Staub, Luxembourg Denis Coulombier, Stockholm, Sweden The FYR of Macedonia: Elisaveta Stikova, Skopje Christian Drosten, Bonn, Germany Malta: Tanya Melillo Fenech, Valletta Karl Ekdahl, Stockholm, Sweden Netherlands: Paul Bijkerk, Bilthoven Johan Giesecke, Stockholm, Sweden Norway: Hilde Klovstad, Oslo Herman Goossens, Antwerp, Belgium Poland: Malgorzata Sadkowska-Todys, Warsaw David Heymann, London, United Kingdom Portugal: Isabel Marinho Falcão, Lisbon Heath Kelly, Melbourne, Australia Romania: Daniela Pitigoi, Bucharest Irena Klavs, Ljubljana, Slovenia Serbia: Tatjana Pekmezovic, Belgrade Karl Kristinsson, Reykjavik, Iceland Scotland: Norman Macdonald, Glasgow Daniel Lévy-Bruhl, Paris, France Slovakia: Lukáš Murajda, Martin Richard Pebody, London, United Kingdom Slovenia: Alenka Kraigher, Ljubljana Panayotis T. Tassios, Athens, Greece Spain: Elena Rodríguez Valín, Madrid Hélène Therre, Paris, France Sweden: Christer Janson, Stockholm Henriette de Valk, Paris, France European Commission: Paolo Guglielmetti, Luxembourg Sylvie van der Werf, Paris, France World Health Organization Regional Office for Europe: Nedret Emiroglu, Copenhagen Design / Layout Fabrice Donguy / Arne Haeger www.eurosurveillance.org © Eurosurveillance, 2012 Editorials From molecular to genomic epidemiology: transforming surveillance and control of infectious diseases M J Struelens ([email protected])1, S Brisse2 1. European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden 2. Institut Pasteur, Paris, France Citation style for this article: Struelens MJ, Brisse S. From molecular to genomic epidemiology: transforming surveillance and control of infectious diseases. Euro Surveill. 2013;18(4):pii=20386. Available online: http://www.eurosurveillance.org/ViewArticle.aspx?ArticleId=20386 Article published on 24 January 2013 The use of increasingly powerful genotyping tools population as possible to identify clusters of clonally for the characterisation of pathogens has become a linked isolates [5]. Examples include PulseNet, the standard component of infectious disease surveil- nationwide food-borne disease surveillance system lance and outbreak investigations. This thematic issue in the United States [7] as well as national molecular of Eurosurveillance, published in two parts, provides surveillance schemes developed to detect clusters a series of review and original research articles that of tuberculosis as described by Fitzgibbon et al. [8]. gauge progress in molecular epidemiology strategies Library typing systems that use more stable genotypic and tools, and illustrate their applications in pub- markers such as bacterial multilocus sequence typing lic health. Molecular epidemiology of infectious dis- (MLST) are suitable for strategy-oriented molecular eases combines traditional epidemiological methods surveillance aimed at monitoring secular trends in the with analysis of genome polymorphisms of pathogens evolution of pathogen genotypes and in their distribu- over time, place and person across human popula- tion over larger geographic and population scales [1-5]. tions and relevant reservoirs, to study host–pathogen Such molecular surveillance systems can call attention interactions and infer hypotheses about host-to-host to the emergence of strains with enhanced virulence or or source-to-host transmission [1-3]. Based on dis- drug resistance, help identify risk factors associated criminant genotyping of human pathogens, clonally with transmission of specific strains, or predict the derived strains can be identified as likely links in a effectiveness of public health measures such as vac- chain of transmission [1-3]. In this two-part issue of cinations. This approach is well established for global Eurosurveillance, Goering et al. explain that such bio- virological surveillance of human and avian influenza. logical evidence of clonal linkage complements but As illustrated by an experience from New-Zealand does not replace epidemiological evidence of person- presented by Muellner et al., a nationwide molecular to-person contact or common exposure to a poten- surveillance of campylobacteriosis using a sequential tial source [3]. Muellner et al. provide clear examples combination of typing systems can inform both disease how prediction about infectious disease outcome and control measures and prevention policies by detecting transmission risks can be enhanced through integra- local outbreaks and modelling endemic disease attri- tion of pathogen genetic information and epidemiologi- bution to specific food sources [4]. Structured sur- cal modelling to inform public health decisions about veys that combine spatiotemporal mapping of strain food-borne disease prevention [4]. genotype and antimicrobial resistance phenotype is a powerful means to monitor the emergence and spread As reviewed by Sabat et al., epidemic source tracing of multidrug-resistant clones across a continent, as requires timely deployment of high resolution typing reported by Chisolm et al. for Neisseria gonorrhoeae in methods that index variation of genomic elements Europe [9]. with a fast molecular clock [1-5]. For outbreak stud- ies, comparative methods, as opposed to library typ- As summarised by Sabat et al., there have been con- ing methods, are sufficient, and the higher the power tinuous technological improvements for microbial to resolve micro-evolutionary distance, the greater the genomic characterisation in the past decade, mov- likelihood to decide between alternative transmission ing from fingerprinting methods such as pulsed-field hypotheses generated by observational epidemiology gel electrophoresis of bacterial macrorestriction [1-6]. Once standardised to enable a uniform genotype fragments to more robust, portable and biologically nomenclature across laboratories, thereby providing informative assays such as bacterial multilocus var- a library typing system, such discriminatory methods iable-number tandem repeat analysis (MLVA) and can be further applied to control-oriented surveillance sequencing of single/multiple loci of both bacterial and [1-5]. Early outbreak detection is achieved by geno- viral human pathogens [3-5,9-11]. With the decreasing typing prospectively as many consecutive cases in a cost and continuing refinement of high-throughput 2 www.eurosurveillance.org genome sequencing technologies, we are now wit- for so-called monomorphic pathogens [5,11]. In addi- nessing a quantum leap from genotypic epidemiology tion, MLVA has a strong potential for inter-laboratory to genomic epidemiology as whole viral or bacterial standardisation, and several web-accessible database genomes become open to scrutiny at population level. systems have been developed [5,10-11]. One important As reviewed by Carrico et al., advances in laboratory drawback is that many MLVA schemes are highly spe- typing tools have been enabled by parallel progress in cific for given clones, thus limiting their applicability. the information technology needed to capture genetic Furthermore, for long-term epidemiology or population data on pathogens, and in quality control, formatting, biology, MLVA markers can be affected by homoplasy, storage, management and, most importantly, bioinfor- which renders MLVA data less robust than MLST as a matics analysis and real-time electronic data sharing library typing system and for phylogenetic purposes. through online databases [10]. It also remains unclear whether assembly of high throughput sequence data will be reliable enough to Among the sequence-based genotyping assays, MLST determine MLVA alleles, as the repeat arrays pose par- is widely applied for epidemiological investigations of ticular technical challenges for current high throughput bacterial and fungal pathogens and is a primary typ- sequencing technologies. ing method for clonal delineation in pathogens such as Neisseria [12] or Campylobacter [4]. The advantages From a perspective of medical and public health micro- of MLST are twofold: firstly, it generates reproducible biology and epidemiology, whole genome sequencing and standardised data that are highly portable (i.e. (WGS) combines two decisive advantages compared easily transferrable