Whole-genome sequencing reveals clonal expansion of multiresistant Staphylococcus haemolyticus in European hospitals

Cavanagh, JP; Hjerde, E; Holden, MTG; Kahlke, T; Klingenberg, C; Flægstad, T; Parkhill, J; Bentley, SD; Ericson Sollid, JU

Whole-genome sequencing reveals clonal expansion of multiresistant Staphylococcus haemolyticus in European hospitals

Cavanagh, JP Hjerde, E Holden, MTG Kahlke, T

Klingenberg, C Flægstad, T Parkhill, J Bentley, SD Ericson Sollid, JU

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Publication Type:: Journal Article
Citation:: Journal of Antimicrobial Chemotherapy, 2014, 69 (11), pp. 2920 - 2927
Issue Date:: 2014-01-01

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Field	Value	Language
dc.contributor.author	Cavanagh, JP	en_US
dc.contributor.author	Hjerde, E	en_US
dc.contributor.author	Holden, MTG	en_US
dc.contributor.author	Kahlke, T https://orcid.org/0000-0002-9762-6573	en_US
dc.contributor.author	Klingenberg, C	en_US
dc.contributor.author	Flægstad, T	en_US
dc.contributor.author	Parkhill, J	en_US
dc.contributor.author	Bentley, SD	en_US
dc.contributor.author	Ericson Sollid, JU	en_US
dc.date.issued	2014-01-01	en_US
dc.identifier.citation	Journal of Antimicrobial Chemotherapy, 2014, 69 (11), pp. 2920 - 2927	en_US
dc.identifier.issn	0305-7453	en_US
dc.identifier.uri	http://hdl.handle.net/10453/118918
dc.description.abstract	© The Author 2014. Objectives: Staphylococcus haemolyticus is an emerging cause of nosocomial infections, primarily affecting immunocompromised patients. A comparative genomic analysis was performed on clinical S. haemolyticus isolates to investigate their genetic relationship and explore the coding sequences with respect to antimicrobial resistance determinants and putative hospital adaptation. Methods: Whole-genome sequencing was performed on 134 isolates of S. haemolyticus from geographically diverse origins (Belgium, 2; Germany, 10; Japan, 13; Norway, 54; Spain, 2; Switzerland, 43; UK, 9; USA, 1). Each genome was individually assembled. Protein coding sequences (CDSs) were predicted and homologous genes were categorized into three types: Type I, core genes, homologues present in all strains; Type II, unique core genes, homologues shared by only a subgroup of strains; and Type III, unique genes, strain-specific CDSs. The phylogenetic relationship between the isolates was built from variable sites in the form of single nucleotide polymorphisms (SNPs) in the core genome and used to construct a maximum likelihood phylogeny. Results: SNPs in the genome core regions divided the isolates into one major group of 126 isolates and one minor group of isolates with highly diverse genomes. The major group was further subdivided into seven clades (A-G), of which four (A-D) encompassed isolates only from Europe. Antimicrobial multiresistance was observed in 77.7% of the collection. High levels of homologous recombination were detected in genes involved in adherence, staphylococcal host adaptation and bacterial cell communication. Conclusions: The presence of several successful and highly resistant clones underlines the adaptive potential of this opportunistic pathogen.	en_US
dc.relation.ispartof	Journal of Antimicrobial Chemotherapy	en_US
dc.relation.isbasedon	10.1093/jac/dku271	en_US
dc.subject.classification	Microbiology	en_US
dc.subject.mesh	Humans	en_US
dc.subject.mesh	Staphylococcus haemolyticus	en_US
dc.subject.mesh	Sequence Analysis, DNA	en_US
dc.subject.mesh	Drug Resistance, Multiple, Bacterial	en_US
dc.subject.mesh	Polymorphism, Single Nucleotide	en_US
dc.subject.mesh	Hospitals	en_US
dc.subject.mesh	Europe	en_US
dc.subject.mesh	Genome-Wide Association Study	en_US
dc.title	Whole-genome sequencing reveals clonal expansion of multiresistant Staphylococcus haemolyticus in European hospitals	en_US
dc.type	Journal Article
utslib.citation.volume	11	en_US
utslib.citation.volume	69	en_US
utslib.for	0605 Microbiology	en_US
utslib.for	1115 Pharmacology and Pharmaceutical Sciences	en_US
utslib.for	1108 Medical Microbiology	en_US
pubs.embargo.period	Not known	en_US
pubs.organisational-group	/University of Technology Sydney
pubs.organisational-group	/University of Technology Sydney/Faculty of Science
pubs.organisational-group	/University of Technology Sydney/Strength - C3 - Climate Change Cluster
utslib.copyright.status	open_access
pubs.issue	11	en_US
pubs.publication-status	Published	en_US
pubs.volume	69	en_US

Abstract:

© The Author 2014. Objectives: Staphylococcus haemolyticus is an emerging cause of nosocomial infections, primarily affecting immunocompromised patients. A comparative genomic analysis was performed on clinical S. haemolyticus isolates to investigate their genetic relationship and explore the coding sequences with respect to antimicrobial resistance determinants and putative hospital adaptation. Methods: Whole-genome sequencing was performed on 134 isolates of S. haemolyticus from geographically diverse origins (Belgium, 2; Germany, 10; Japan, 13; Norway, 54; Spain, 2; Switzerland, 43; UK, 9; USA, 1). Each genome was individually assembled. Protein coding sequences (CDSs) were predicted and homologous genes were categorized into three types: Type I, core genes, homologues present in all strains; Type II, unique core genes, homologues shared by only a subgroup of strains; and Type III, unique genes, strain-specific CDSs. The phylogenetic relationship between the isolates was built from variable sites in the form of single nucleotide polymorphisms (SNPs) in the core genome and used to construct a maximum likelihood phylogeny. Results: SNPs in the genome core regions divided the isolates into one major group of 126 isolates and one minor group of isolates with highly diverse genomes. The major group was further subdivided into seven clades (A-G), of which four (A-D) encompassed isolates only from Europe. Antimicrobial multiresistance was observed in 77.7% of the collection. High levels of homologous recombination were detected in genes involved in adherence, staphylococcal host adaptation and bacterial cell communication. Conclusions: The presence of several successful and highly resistant clones underlines the adaptive potential of this opportunistic pathogen.

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http://hdl.handle.net/10453/118918