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Epidemiological aspects of healthcare-associated infections and microbial genomics

  • C. MirandeEmail author
  • I. Bizine
  • A. Giannetti
  • N. Picot
  • A. van Belkum
Review

Abstract

Hospital-acquired infections (HAIs) are a cause of continuously increasing morbidity and mortality. Most of these infections are caused by a limited set of bacterial species, which share the capability to efficiently spread from patient to patient and to easily acquire antibiotic resistance determinants. This renders correct and rapid species identification and antibiotic susceptibility testing (AST) important and underscores the relevance of bacterial epidemiological typing. The latter is needed for the sensitive detection and exact tracing of nosocomial spread of these potentially multidrug-resistant microorganisms (MDRO). Many microbial typing technologies have been developed and put to some level of executive practice, but it seems that the continued evolution in methodology has currently reached an apex: there is likely to be scientific and practical consensus on the ultimate typing potential of bacterial whole-genome sequencing (WGS). The possibility to perform pan-genomic nucleotide-to-nucleotide comparisons between strains belonging to a single species and to detect even minute changes in nucleotide order will identify closely related organisms, while upon accumulation of such mutations, independent descend can be assumed. Calibration of difference levels [i.e. number of single nucleotide polymorphisms (SNPs)] into categories of inter-strain relatedness needs to be performed in order to generate robust, portable typing schemes. Here, we will briefly discuss the state of affairs regarding bacterial epidemiology based upon WGS, its relatedness with the nomenclature of former typing approaches and the continuing need for a global typing language.

Notes

Acknowledgements

We would like to acknowledge the much appreciated help of many of our colleagues from bioMérieux Microbiology Research and Development and the bioMérieux Data Analytics Unit.

Funding

No external funding was acquired in the context of the work described in the present publication.

Compliance with ethical standards

Conflict of interest

All authors were or still are employees of bioMérieux, a company developing and selling infectious disease diagnostics.

Ethics approval and informed consent

Not applicable.

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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  • C. Mirande
    • 1
    Email author
  • I. Bizine
    • 1
  • A. Giannetti
    • 1
  • N. Picot
    • 2
  • A. van Belkum
    • 3
  1. 1.Research and Development MicrobiologybioMérieuxLa Balme Les GrottesFrance
  2. 2.IP and Scientific Watch DepartmentbioMérieuxMarcy l’EtoileFrance
  3. 3.Data Analytics UnitbioMérieuxLa Balme Les GrottesFrance

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