Eurosurveillance - Volume 13, Issue 19, 08 May 2008

By providing appropriate discriminatory analyses, molecular typing can foster rapid and – depending on the method – even real-time early detection of dispersed international clusters/outbreaks, the detection and investigation of transmission chains, the relatedness of strains, and the emergence of antimicrobial resistance and new evolving pathogenic strains.

Although vaccine-preventable, rabies remains a worldwide-occurring disease of major public health concern. Globally, rabies is responsible for about 55,000 human deaths per year, mainly in Asia and Africa, and 30-50% of the cases are in children, most often following an infection transmitted through the bite of a rabid dog.

On the evening of 25 April 2008, the Health Protection Agency of the United Kingdom (UK) was informed that rabies had been confirmed through post-mortem examination of a dog that had died that same day in a quarantine centre in London. The dog, approximately 10 weeks old, had been imported from Sri Lanka, through Heathrow Airport in London, on 17 April by a charity that 'rescues' stray animals from that country and imports them into the UK. The public health response was undertaken through the coordinated activities of the authorities responsible for animal and human public health respectively. .

The HARMONY typing network was part of the European Union (EU) Directorate General XII (now the Directorate-General for Research) funded project 'Harmonisation of Antibiotic Resistance measurement, Methods of typing Organisms and ways of using these and other tools to increase the effectiveness of Nosocomial Infection control', awarded in 1999. Other aspects of the project comprised the exploration of the feasibility of developing a consensual approach to infection control guidelines, examining the issues of antimicrobial susceptibility standardisation and developing a tool to facilitate the establishment of effective antibiotic stewardship [1,2]. Many of the typing group participants were also members of the International Union of Microbiology Societies' (IUMS) Staphylococcal Sub-Committee. This was established in the 1970s to ensure that phage typing was standardised globally and to provide propagating phages for phage-typing [3]. Over time phage-typing had become less useful for some strains of methicillin-resistant and, indeed, methicillin-sensitive, Staphylococcus aureus (MRSA and MSSA), as they had become non phage-typable [3]. The IUMS Staphylococcal Sub-Committee now included reference laboratories and centres of staphylococcal research excellence with interests in typing staphylococci by molecular techniques which were more effective than phage for typing some staphylococci. When we started the HARMONY project, it was at a time of tremendous advances in molecular typing methods and we thus added new techniques to the HARMONY assessment process as these became relevant and practical propositions. There were also other aims such as, for example, agreeing criteria for referral of isolates to a typing laboratory and an approach to the nomenclature of MRSA strains. .

SeqNet.org is currently an initiative of 44 laboratories from 25 European countries and one laboratory from Lebanon (Table 1), founded in 2004, in collaboration with the Robert Koch Institute at the University of Münster, Germany (http://www.SeqNet.org). Since then, its main objective is to establish a European network of excellence for sequence-based typing of microbial pathogens, having its main focus on Staphylococcus aureus [1]. SeqNet.org comprises a large number of national reference laboratories as well as university laboratories. The principle goal of SeqNet.org is to generate unambiguous, easily comparable typing data in electronic, portable form to be used by infection control at a local level as well as national and European surveillance of sentinel micro-organisms, such as methicillin-resistant Staphylococcus aureus (MRSA). spa-typing has been shown to be a useful tool in molecular hospital epidemiology [2,3]. Veterinary laboratories have recently joined the SeqNet.org initiative as MRSA has become an emerging problem in veterinary medicine [4,5]. spa-typing data from human and veterinary medicine can be compared using the spa server database [6]. .

Strain typing is an important aid to surveillance networks and outbreak investigations of infectious diseases [1]. MLVA (Multilocus VNTR Analysis, with VNTR standing for Variable Number of Tandem Repeats) has emerged as a highly discriminatory and widely applicable genotyping method that is now being applied for strain tracking in a growing number of bacterial pathogens [2,3]. The genomic loci containing tandem repeats are often maintained among strains of a bacterial species, while individual strains harbour different copy numbers that can be determined simply by PCR amplification. Similar to sequence-based methods such as Multilocus Sequence Typing (MLST), the MLVA method indexes genetic variation at well defined genomic loci and produces reproducible allelic profiles that can be coded in a simple digital format. Hence, they represent an attractive alternative to banding profile-based methods such as pulsed-field gel electrophoresis (PFGE), which requires dedicated efforts (e.g. http://www.cdc.gov/pulsenet) in order to produce fingerprinting data that are comparable across laboratories. Indeed, to be useful to surveillance networks and for global epidemiology, a genotyping method has to be technically accessible, reproducible and to yield easily portable data. In addition, electronic databases that are made accessible through the Internet can render exchange and comparison of data among laboratories very effective for local, national, and international surveillance. Existing databases of MLST data accessible through web portals (http://www.pubmlst.org,http://www.mlst.net, http://www.pasteur.fr/mlst) represent a common language for strain typing that has proven extremely useful for collaborative research and global epidemiology of bacterial and fungal pathogens [4]. However, given the much faster evolutionary rate of tandem repeats compared to nucleotide sequences, MLVA markers provide much improved resolution compared to MLST, thus representing a subtyping tool that is especially useful for strain discrimination in genetically homogeneous pathogens, such as M. tuberculosis [5], Bacillus anthracis [6] or Salmonella enterica serotype Typhimurium [7]. Web-accessible MLVA databases are not yet widely used for international collaboration [8], but the development in this area is very active (http://mlva.u-psud.fr/, http://www.mlva.eu/, http://www.miru-vntrplus.org).

The Diphtheria Surveillance Network (DIPNET), launched on 1 November 2006, is a 38-month programme bringing together 25 European Union partner countries (24 Member States and Turkey) and collaborating countries beyond Europe in a global dedicated surveillance network for diphtheria and related infections caused by Corynebacterium diphtheriae and C. ulcerans [1].

Measles virus causes an acute infection characterised by rash and fever. Measles infection is preventable by vaccination, but remains a significant cause of childhood mortality in the developing world with an estimated number of approximately 242,000 deaths by measles in 2006 [1].

Hepatitis B virus (HBV) is a major human pathogen. The outcome of acute hepatitis B is variable but usually followed by a complete recovery. A small proportion of infections in adults and a higher proportion of infections in early childhood continue in a chronically infected state in which the virus persists in the liver. Patients with chronic hepatitis B usually have no initial symptoms of infection, but over time the major disease sequelae, cirrhosis and hepatocellular carcinoma, can develop. It is estimated that some 350 million people worldwide are currently chronically infected with HBV, but many more will have been infected and recovered.

The FBVE (Food-borne Viruses in Europe) network was initiated during a research project funded by the European Commission (contract QLK1-1999-00594). The aim of the network is to establish a framework for rapid, (pre-publication) exchange of epidemiological, virological and molecular diagnostic data on outbreaks of viral gastroenteritis and acute hepatitis due to hepatitis A and E viruses for both surveillance and research purposes.

The panel on biological hazards (BIOHAZ) of the European Food Safety Authority (EFSA) published a draft opinion recently on the extent to which food serves as a vehicle for antimicrobial resistance.