2018
DOI: 10.1186/s13073-018-0593-7
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Whole-genome epidemiology, characterisation, and phylogenetic reconstruction of Staphylococcus aureus strains in a paediatric hospital

Abstract: BackgroundStaphylococcus aureus is an opportunistic pathogen and a leading cause of nosocomial infections. It can acquire resistance to all the antibiotics that entered the clinics to date, and the World Health Organization defined it as a high-priority pathogen for research and development of new antibiotics. A deeper understanding of the genetic variability of S. aureus in clinical settings would lead to a better comprehension of its pathogenic potential and improved strategies to contrast its virulence and … Show more

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Cited by 66 publications
(80 citation statements)
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References 181 publications
(192 reference statements)
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“…Indeed, as different bacterial lineages may harbor largely different gene sets (and hence different functional capacities) [68], strain-level profiling may provide a more complete picture of microbiota dynamics in CF. Relevant bacterial species in CF, such as P. aeruginosa [69] and Staphylococcus aureus [70,71], possess large, flexible gene pools, including genes encoding antibiotic resistance, pathogenicity, environmental response, and metabolic flexibility, which may explain the adaptive nature of chronic infections [72]. Although the metagenome contributes greatly to interactions with the host [25,73], very few studies on CF metagenomes have been performed, involving a limited number of both patients [29,63,74,75] and specific metabolic functions [76].…”
Section: Many Singers But Which Song(s)?mentioning
confidence: 99%
“…Indeed, as different bacterial lineages may harbor largely different gene sets (and hence different functional capacities) [68], strain-level profiling may provide a more complete picture of microbiota dynamics in CF. Relevant bacterial species in CF, such as P. aeruginosa [69] and Staphylococcus aureus [70,71], possess large, flexible gene pools, including genes encoding antibiotic resistance, pathogenicity, environmental response, and metabolic flexibility, which may explain the adaptive nature of chronic infections [72]. Although the metagenome contributes greatly to interactions with the host [25,73], very few studies on CF metagenomes have been performed, involving a limited number of both patients [29,63,74,75] and specific metabolic functions [76].…”
Section: Many Singers But Which Song(s)?mentioning
confidence: 99%
“…SNV analysis is frequently used to type isolates based on WGS data in an outbreak scenario and has been used extensively using data generated by short read sequencers such as those manufactured by Illumina [12][13][14][15][22][23][24]. This approach involves mapping sequence reads or larger contiguous sequences (known as contigs) assembled from overlapping short read sequences to a reference genome by core genome alignment.…”
Section: Single Nucleotide Variation Analysismentioning
confidence: 99%
“…By next generation sequencing (NGS) technology, the whole genome sequencing (WGS) of pathogen microorganisms has been introduced improving the ability to identify and control epidemic outbreaks, thus preventing the spread of the pathogen and decreasing morbidity and mortality . Phylogenetic analysis applied to whole genome sequences has been used for the epidemiological surveillance of nosocomial infections as recently reported …”
Section: Phylogenetic Analysis Of Whole‐genome Sequencing For Viral Nmentioning
confidence: 99%
“…236 Phylogenetic analysis applied to whole genome sequences has been used for the epidemiological surveillance of nosocomial infections as recently reported. 3,4,237 F I G U R E 5 A, Mathematical evolutionary modeling applied on protein sequence. B, Structure analysis to make a prevision on the effect of selective pressure…”
Section: Phylogenetic Analysis Of Whole-genome Sequencing For Viralmentioning
confidence: 99%