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

Cooper, Jessica E.; Feil, Edward J.

doi:10.1099/mic.0.28620-0

Cited by 60 publications

(66 citation statements)

References 41 publications

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“…These results confirmed that the improved MLST scheme has a better discriminatory ability than the previous ones and should be adopted henceforth as the unique and universal S. epidermidis MLST scheme (4).…”

Section: Discussionsupporting

confidence: 76%

Inferring a Population Structure for Staphylococcus epidermidis from Multilocus Sequence Typing Data

et al. 2007

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Despite its importance as a human pathogen, information on population structure and global epidemiology of Staphylococcus epidermidis is scarce and the relative importance of the mechanisms contributing to clonal diversification is unknown. In this study, we addressed these issues by analyzing a representative collection of S. epidermidis isolates from diverse geographic and clinical origins using multilocus sequence typing (MLST). Additionally, we characterized the mobile element (SCCmec) carrying the genetic determinant of methicillin resistance. The 217 S. epidermidis isolates from our collection were split by MLST into 74 types, suggesting a high level of genetic diversity. Analysis of MLST data using the eBURST algorithm revealed the existence of nine epidemic clonal lineages that were disseminated worldwide. One single clonal lineage (clonal complex 2) comprised 74% of the isolates, whereas the remaining isolates were clustered into 8 minor clonal lineages and 13 singletons. According to our evolutionary model, SCCmec was acquired at least 56 times by S. epidermidis. Although geographic dissemination of S. epidermidis strains and the value of the index of association between the alleles, 0.2898 (P < 0.05), support the clonality of S. epidermidis species, examination of the sequence changes at MLST loci during clonal diversification showed that recombination gives rise to new alleles approximately twice as frequently as point mutations. We suggest that S. epidermidis has a population with an epidemic structure, in which nine clones have emerged upon a recombining background and evolved quickly through frequent transfer of genetic mobile elements, including SCCmec.

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Section: Discussionsupporting

confidence: 76%

Inferring a Population Structure for Staphylococcus epidermidis from Multilocus Sequence Typing Data

et al. 2007

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“…In other words, strains within our sample of the population in one square metre of soil can be more diverged from each other in these replicons than from a strain originating 41600 km away in very different climatic conditions. It is usual that genes of accessory or unknown function, which are frequent on extrachromosomal replicons, are more polymorphic than core genes that may be under strong purifying selection (for example, Cooper and Feil (2006)), but it is interesting to observe that this polymorphism extends to local populations and not just wider strain collections. Of course, we are looking here at nucleotide divergence of genes that are shared by all strains, rather than at the presence or absence of potentially adaptive accessory genes, which are discussed in the next section.…”

Section: Discussionmentioning

confidence: 99%

Population genomics of Sinorhizobium medicae based on low-coverage sequencing of sympatric isolates

et al. 2011

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We investigated the genomic diversity of a local population of the symbiotic bacterium Sinorhizobium medicae, isolated from the roots of wild Medicago lupulina plants, in order to assess genomic diversity, to identify genomic regions influenced by duplication, deletion or strong selection, and to explore the composition of the pan-genome. Partial genome sequences of 12 isolates were obtained by Roche 454 shotgun sequencing (average 5.3 Mb per isolate) and compared with the published sequence of S. medicae WSM 419. Homologous recombination appears to have less impact on the polymorphism patterns of the chromosome than on the chromid pSMED01 and megaplasmid pSMED02. Moreover, pSMED02 is a hot spot of insertions and deletions. The whole chromosome is characterized by low sequence polymorphism, consistent with the high density of housekeeping genes. Similarly, the level of polymorphism of symbiosis genes (low) and of genes involved in polysaccharide synthesis (high) may reflect different selection. Finally, some isolates carry genes that may confer adaptations that S. medicae WSM 419 lacks, including homologues of genes encoding rhizobitoxine synthesis, iron uptake, response to autoinducer-2, and synthesis of distinct polysaccharides. The presence or absence of these genes was confirmed by PCR in each of these 12 isolates and a further 27 isolates from the same population. All isolates had rhizobitoxine genes, while the other genes were co-distributed, suggesting that they may be on the same mobile element. These results are discussed in relation to the ecology of Medicago symbionts and in the perspective of population genomics studies.

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“…adhesion genes) are at least as informative for phylogenetic reconstruction as the more slowly evolving housekeeping genes (e.g. MLST) [19][20][21][22][23].…”

Section: Discussionmentioning

confidence: 99%

High-throughput typing of Staphylococcus aureus by amplified fragment length polymorphism (AFLP) or multi-locus variable number of tandem repeat analysis (MLVA) reveals consistent strain relatedness

Melles∗

Schouls

François

et al. 2008

Eur J Clin Microbiol Infect Dis

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This study investigates aspects of the general assumption that, in bacteria, genetic variation in functionally-constrained genomic regions accumulates at a lower rate than in regions of hypermutability such as DNA repeat loci. We compared whole genome polymorphism (using high-throughput amplified fragment length polymorphism [ht-AFLP]) as well as short sequence repeat length variation (using multi-locus variable number of tandem repeat analysis [MLVA]) for 994 Staphylococcus aureus strains isolated from both healthy carriers and invasive infections. MLVA and ht-AFLP minimum spanning trees (MSTs) were similar in their identification of totally different types of genetic variants. This suggests that, despite the enhanced inherent variability of repeats, clusters of strains remain traceable. Finally, no specific molecular marker of epidemicity or virulence was identified in this large strain collection by the MLVA approach. We demonstrate that there is a difference in the rates of cross-genome mutation versus regional repeat variability in the clonal bacterial pathogen S. aureus. Despite these dynamic differences, a conservation of type assignments as based upon these two inherently different typing techniques was observed.

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

Cited by 60 publications

References 41 publications

Inferring a Population Structure for Staphylococcus epidermidis from Multilocus Sequence Typing Data

Inferring a Population Structure for Staphylococcus epidermidis from Multilocus Sequence Typing Data

Population genomics of Sinorhizobium medicae based on low-coverage sequencing of sympatric isolates

High-throughput typing of Staphylococcus aureus by amplified fragment length polymorphism (AFLP) or multi-locus variable number of tandem repeat analysis (MLVA) reveals consistent strain relatedness

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