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Core genome conservation of Staphylococcus haemolyticus limits sequence based population structure analysis

Cavanagh, Jorunn Pauline
Klingenberg, Claus
Hanssen, Anne-Merethe
Fredheim, Elizabeth Aarag
Flægstad, Trond
Sollid, Johanna Ericson
Published in Journal of microbiological methods. 2012, vol. 89, no. 3, p. 159-66
Abstract The notoriously multi-resistant Staphylococcus haemolyticus is an emerging pathogen causing serious infections in immunocompromised patients. Defining the population structure is important to detect outbreaks and spread of antimicrobial resistant clones. Currently, the standard typing technique is pulsed-field gel electrophoresis (PFGE). In this study we describe novel molecular typing schemes for S. haemolyticus using multi locus sequence typing (MLST) and multi locus variable number of tandem repeats (VNTR) analysis. Seven housekeeping genes (MLST) and five VNTR loci (MLVF) were selected for the novel typing schemes. A panel of 45 human and veterinary S. haemolyticus isolates was investigated. The collection had diverse PFGE patterns (38 PFGE types) and was sampled over a 20 year-period from eight countries. MLST resolved 17 sequence types (Simpsons index of diversity [SID]=0.877) and MLVF resolved 14 repeat types (SID=0.831). We found a low sequence diversity. Phylogenetic analysis clustered the isolates in three (MLST) and one (MLVF) clonal complexes, respectively. Taken together, neither the MLST nor the MLVF scheme was suitable to resolve the population structure of this S. haemolyticus collection. Future MLVF and MLST schemes will benefit from addition of more variable core genome sequences identified by comparing different fully sequenced S. haemolyticus genomes.
Keywords AnimalsCluster AnalysisConserved SequenceDNA, Bacterial/chemistry/geneticsGenes, BacterialGenome, BacterialHumansMolecular Typing/methodsPolymorphism, GeneticStaphylococcal Infections/microbiology/veterinaryStaphylococcus haemolyticus/classification/genetics/isolation & purification
PMID: 22484086
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Article (Published version) (400 Kb) - public document Free access
Research group Analyse génomique et fonctionnelle du staphylocoque doré (604)
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CAVANAGH, Jorunn Pauline et al. Core genome conservation of Staphylococcus haemolyticus limits sequence based population structure analysis. In: Journal of microbiological methods, 2012, vol. 89, n° 3, p. 159-66. doi: 10.1016/j.mimet.2012.03.014 https://archive-ouverte.unige.ch/unige:28374

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Deposited on : 2013-06-04

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