Giuseppe
Emeritus
[Source: Eurosurveillance, full text: (LINK). Abstract, edited.]
A J Sabat<SUP>1</SUP>, A Budimir<SUP>2</SUP>, D Nashev<SUP>3</SUP>, R S?-Le?o<SUP>4</SUP>, J M van Dijl<SUP>1</SUP>, F Laurent<SUP>5</SUP>, H Grundmann<SUP>1</SUP>, A W Friedrich (
)<SUP>1</SUP>, on behalf of the ESCMID Study Group of Epidemiological Markers (ESGEM)<SUP>6</SUP>
Citation style for this article: Sabat AJ, Budimir A, Nashev D, S?-Le?o R, van Dijl JM, Laurent F, Grundmann H, Friedrich AW, on behalf of the ESCMID Study Group of Epidemiological Markers (ESGEM). Overview of molecular typing methods for outbreak detection and epidemiological surveillance. Euro Surveill. 2013;18(4)
ii=20380. Available online: http://www.eurosurveillance.org/ViewArticle.aspx?ArticleId=20380
Date of submission: 30 June 2012 <HR>Typing methods for discriminating different bacterial isolates of the same species are essential epidemiological tools in infection prevention and control. Traditional typing systems based on phenotypes, such as serotype, biotype, phage-type, or antibiogram, have been used for many years. However, more recent methods that examine the relatedness of isolates at a molecular level have revolutionised our ability to differentiate among bacterial types and subtypes. Importantly, the development of molecular methods has provided new tools for enhanced surveillance and outbreak detection. This has resulted in better implementation of rational infection control programmes and efficient allocation of resources across Europe. The emergence of benchtop sequencers using next generation sequencing technology makes bacterial whole genome sequencing (WGS) feasible even in small research and clinical laboratories. WGS has already been used for the characterisation of bacterial isolates in several large outbreaks in Europe and, in the near future, is likely to replace currently used typing methodologies due to its ultimate resolution. However, WGS is still too laborious and time-consuming to obtain useful data in routine surveillance. Also, a largely unresolved question is how genome sequences must be examined for epidemiological characterisation. In the coming years, the lessons learnt from currently used molecular methods will allow us to condense the WGS data into epidemiologically useful information. On this basis, we have reviewed current and new molecular typing methods for outbreak detection and epidemiological surveillance of bacterial pathogens in clinical practice, aiming to give an overview of their specific advantages and disadvantages.
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Eurosurveillance, Volume 18, Issue 4, 24 January 2013
Review articles
Overview of molecular typing methods for outbreak detection and epidemiological surveillance
Review articles
Overview of molecular typing methods for outbreak detection and epidemiological surveillance
A J Sabat<SUP>1</SUP>, A Budimir<SUP>2</SUP>, D Nashev<SUP>3</SUP>, R S?-Le?o<SUP>4</SUP>, J M van Dijl<SUP>1</SUP>, F Laurent<SUP>5</SUP>, H Grundmann<SUP>1</SUP>, A W Friedrich (
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Department of Clinical Microbiology and Molecular Microbiology, Clinical Hospital Centre Zagreb, Zagreb, Croatia
- Department of Microbiology, National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Quimica e Biologica, Oeiras, Portugal
- Department of Bacteriology, National Reference Centre for Staphylococci, Inserm U81, Hospices Civils de Lyon, University of Lyon, Lyon, France
- European Society for Clinical Microbiology and Infectious Diseases, Basel, Switzerland
Citation style for this article: Sabat AJ, Budimir A, Nashev D, S?-Le?o R, van Dijl JM, Laurent F, Grundmann H, Friedrich AW, on behalf of the ESCMID Study Group of Epidemiological Markers (ESGEM). Overview of molecular typing methods for outbreak detection and epidemiological surveillance. Euro Surveill. 2013;18(4)
ii=20380. Available online: http://www.eurosurveillance.org/ViewArticle.aspx?ArticleId=20380 Date of submission: 30 June 2012 <HR>Typing methods for discriminating different bacterial isolates of the same species are essential epidemiological tools in infection prevention and control. Traditional typing systems based on phenotypes, such as serotype, biotype, phage-type, or antibiogram, have been used for many years. However, more recent methods that examine the relatedness of isolates at a molecular level have revolutionised our ability to differentiate among bacterial types and subtypes. Importantly, the development of molecular methods has provided new tools for enhanced surveillance and outbreak detection. This has resulted in better implementation of rational infection control programmes and efficient allocation of resources across Europe. The emergence of benchtop sequencers using next generation sequencing technology makes bacterial whole genome sequencing (WGS) feasible even in small research and clinical laboratories. WGS has already been used for the characterisation of bacterial isolates in several large outbreaks in Europe and, in the near future, is likely to replace currently used typing methodologies due to its ultimate resolution. However, WGS is still too laborious and time-consuming to obtain useful data in routine surveillance. Also, a largely unresolved question is how genome sequences must be examined for epidemiological characterisation. In the coming years, the lessons learnt from currently used molecular methods will allow us to condense the WGS data into epidemiologically useful information. On this basis, we have reviewed current and new molecular typing methods for outbreak detection and epidemiological surveillance of bacterial pathogens in clinical practice, aiming to give an overview of their specific advantages and disadvantages.