Determining the Genetic Structure of the Natural Population of Staphylococcus aureus : a Comparison of Multilocus Sequence Typing with Pulsed-Field Gel Electrophoresis, Randomly Amplified Polymorphic DNA Analysis, and Phage Typing

Abstract

We used a sample of Staphylococcus aureus strains that are carried by humans and that are representative of the natural population of S. aureus strains in order to assess the value of multilocus sequence typing (MLST), pulsed-field gel electrophoresis, randomly amplified polymorphic DNA analysis, and phage typing as epidemiological tools. Only MLST was able to define clonal complexes unambiguously. All DNA-based typing approaches achieved a high degree of agreement, implying phylogenetic concordance, but predicted epidemiological associations with variable accuracy.Staphylococcus aureus is one of the most important pathogens in clinical settings. It is also one of the leading causes of nosocomial infections and the dissemination of multipledrug-resistant strains, mainly methicillin-resistant S. aureus (MRSA), and the recent emergence of a vancomycin-resistant MRSA is of concern to hospitals worldwide. Naturally, an understanding of the dynamics of spread and an identification of transmissions or outbreaks are of interest not only to public health epidemiologists but also to clinical microbiologists and indeed clinicians involved in patient management on a daily basis. Most of the current epidemiological typing schemes compare fragment patterns generated by restriction or amplification of chromosomal DNA or by differences in lysis patterns based on susceptibilities to lytic bacteriophages. All of these approaches are able to distinguish between unrelated strains (albeit with different precision), but the probability with which two indistinguishable patterns predict an epidemiological relationship, i.e., transmission, cannot be determined without knowledge of the underlying genetic structure of the naturally occurring population. In order to describe the genetic structure of bacterial populations and the abundance of certain clones in a given environment, typing tools such as multilocus sequence typing (MLST) provide a comprehensive genetic framework (1, 6). We used MLST and three other conventional epidemiological typing approaches to describe the genetic population structure of strains that were systematically collected from nonhospitalized individuals in the community. This way we were able to objectively assess the value of typing techniques deployed for epidemiological purposes.

The phylogeny of Staphylococcus aureus – which genes make the best intra-species markers?

“…Therefore we feel that the intra-species tree we present here would not be greatly improved by the addition of yet more data. The broad consistency of this phylogeny with the basic groupings previously inferred from MLST genes (Feil et al, 2003), sas genes (Robinson et al, 2005), adhesin genes (Kuhn et al, 2006), AFLP clustering (Melles et al, 2004), PFGE (Grundmann et al, 2002) and microarray analysis (Lindsay et al, 2006) provides additional support.…”

“…The current MLST scheme for S. aureus has proved extremely successful in understanding the population structure of this species and for assigning isolates to particular lineages. In a highly clonal organism, almost any gene will typically provide the same basic lineage assignments -in the case of S. aureus this is clear from the broad consistency of different genes as well as pan-genome techniques such as PFGE (Grundmann et al, 2002) and microarrary analysis (Lindsay et al, 2006). However, individual genes may vary in their utility to reconstruct the relationships between these lineages, and we find no evidence to suggest that MLST genes can be considered the most reliable in this regard.…”

Subtyping of ST22-MRSA-IV (Barnim epidemic MRSA strain) at a university clinic in Germany from 2002 to 2005

“…There are only a few pandemic MRSA clones, the so-called Iberian, Brazilian, Hungarian, New York/Japan, paediatric, and epidemic MRSA (EMRSA)-15 and -16 clones, named after the geographical area where they were first identified or according to epidemiological characteristics. The strains of these successful lineages are responsible for most hospitalacquired MRSA infections all over the world today (Enright et al, 2002;Robinson & Enright, 2003). In this regard, the Barnim EMRSA strain (ST22-MRSA-IV) in Germany is ancestral to the UK EMRSA-15 strain (Murchan et al, 2003;Witte et al, 2001).…”

Characterization of 26 Isolates of Staphylococcus Aureus, Predominantly from Dairy Sheep, Using Four Different Techniques of Molecular Epidemiology

“…Moreover, MLST is an adequate technique for generating genetic profiles of a large number of isolates, especially when comparing large international strain collections. 6 For ovine isolates of S. aureus, the RFLP and RAPD techniques used in this report were not suitable as replacements for PFGE but could be useful in combination with PFGE to define strain differentiation.…”