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April 11, 2017

The recent emergence in hospitals of multidrug-resistant community-associated sequence type 1 and spa type t127 methicillin-resistant Staphylococcus aureus investigated by whole-genome sequencing: Implications for screening.

Community-associated spa type t127/t922 methicillin-resistant Staphylococcus aureus (MRSA) prevalence increased from 1%-7% in Ireland between 2010-2015. This study tracked the spread of 89 such isolates from June 2013-June 2016. These included 78 healthcare-associated and 11 community associated-MRSA isolates from a prolonged hospital outbreak (H1) (n = 46), 16 other hospitals (n = 28), four other healthcare facilities (n = 4) and community-associated sources (n = 11). Isolates underwent antimicrobial susceptibility testing, DNA microarray profiling and whole-genome sequencing. Minimum spanning trees were generated following core-genome multilocus sequence typing and pairwise single nucleotide variation (SNV) analysis was performed. All isolates were sequence…

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April 1, 2017

Staphylococcus aureus CC395 harbours a novel composite staphylococcal cassette chromosome mec element.

CoNS species are likely reservoirs of the staphylococcal cassette chromosome mec (SCC mec ) in Staphylococcus aureus . S . aureus CC395 is unique as it is capable of exchanging DNA with CoNS via bacteriophages, which are also known to mediate transfer of SCC mec .To analyse the structure and putative origin of the SCC mec element in S . aureus CC395.The only MRSA CC395 strain described in the literature, JS395, was subjected to WGS, and its SCC mec element was compared with those found in CoNS species and other S. aureus strains.JS395 was found to carry an unusually large…

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February 28, 2017

Genomic analysis of ST88 community-acquired methicillin resistant Staphylococcus aureus in Ghana.

The emergence and evolution of community-acquired methicillin resistant Staphylococcus aureus (CA-MRSA) strains in Africa is poorly understood. However, one particular MRSA lineage called ST88, appears to be rapidly establishing itself as an "African" CA-MRSA clone. In this study, we employed whole genome sequencing to provide more information on the genetic background of ST88 CA-MRSA isolates from Ghana and to describe in detail ST88 CA-MRSA isolates in comparison with other MRSA lineages worldwide.We first established a complete ST88 reference genome (AUS0325) using PacBio SMRT sequencing. We then used comparative genomics to assess relatedness among 17 ST88 CA-MRSA isolates recovered from patients…

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February 23, 2017

Complete genome and plasmid sequences of Staphylococcus aureus EDCC 5055 (DSM 28763), used to study implant-associated infections.

Staphylococcus aureus EDCC 5055 (DSM 28763) is a human clinical wound isolate intensively used to study implant-associated infections in rabbit and rat infection models. Here, we report its complete genome sequence (2,794,437 bp) along with that of one plasmid (27,437 bp). This strain belongs to sequence type 8 and contains a mecA gene. Copyright © 2017 Mannala et al.

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February 9, 2017

DNA target recognition domains in the Type I restriction and modification systems of Staphylococcus aureus.

Staphylococcus aureus displays a clonal population structure in which horizontal gene transfer between different lineages is extremely rare. This is due, in part, to the presence of a Type I DNA restriction–modification (RM) system given the generic name of Sau1, which maintains different patterns of methylation on specific target sequences on the genomes of different lineages. We have determined the target sequences recognized by the Sau1 Type I RM systems present in a wide range of the most prevalent S. aureus lineages and assigned the sequences recognized to particular target recognition domains within the RM enzymes. We used a range…

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October 11, 2016

Complete circular genome sequence of successful ST8/SCCmecIV community-associated methicillin-resistant Staphylococcus aureus (OC8) in Russia: one-megabase genomic inversion, IS256’s spread, and evolution of Russia ST8-IV.

ST8/SCCmecIV community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) has been a common threat, with large USA300 epidemics in the United States. The global geographical structure of ST8/SCCmecIV has not yet been fully elucidated. We herein determined the complete circular genome sequence of ST8/SCCmecIVc strain OC8 from Siberian Russia. We found that 36.0% of the genome was inverted relative to USA300. Two IS256, oppositely oriented, at IS256-enriched hot spots were implicated with the one-megabase genomic inversion (MbIN) and vSaß split. The behavior of IS256 was flexible: its insertion site (att) sequences on the genome and junction sequences of extrachromosomal circular DNA were all…

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July 28, 2016

Complete genome sequences of two methicillin-sensitive Staphylococcus aureus isolates representing a population subset highly prevalent in human colonization.

Here, we report the high-quality draft genome sequences of two methicillin-susceptible Staphylococcus aureus isolates, 08-02119 and 08-02300. Belonging to sequence type 582 (ST582) and ST7, both isolates are representatives of clonal lineages often associated with asymptomatic colonization of humans. Copyright © 2016 Weber et al.

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July 25, 2016

Complete genome sequence of Enterococcus faecalis LD33, a bacteriocin-producing strain.

Enterococcus faecalis LD33 strain was originally isolated from traditional naturally fermented cream in Inner Mongolia of China. Its complete genome sequence was carried out using the Illumina Hiseq and the PacBio RSII platform. The genome only has a circular chromosome and a GC content of 37.58%. Other core information shown in the genome sequencing results further insight on this bacterium's genetic elements for bacteriocin production and the genes related to respiratory chain. Copyright © 2016 Elsevier B.V. All rights reserved.

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May 1, 2016

First report of cfr-encoding plasmids in the pandemic sequence type (ST) 22 methicillin-resistant Staphylococcus aureus Staphylococcal cassette chromosome mec type-IV clone.

Linezolid is often the drug of last resort for serious methicillin-resistant Staphylococcus aureus (MRSA) infections. Linezolid resistance is mediated by mutations in 23S rRNA and genes for ribosomal proteins, cfr encoding phenicol, lincosamide, oxazolidinone, pleuromutilin and streptogramin A (PhLOPSA) resistance, its homolgue cfr(B) or optrA conferring oxazolidinone and phenicol resistance. Linezolid resistance is rare in S. aureus, and cfr even rarer. This study investigated the clonality and linezolid resistance mechanisms of two MRSA isolates from patients in separate Irish hospitals. Isolates were subjected to cfr PCR, PhLOPSA susceptibility testing, 23S rRNA PCR and sequencing, DNA microarray profiling, spa typing, pulsed-field…

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April 28, 2016

PEPR: pipelines for evaluating prokaryotic references.

The rapid adoption of microbial whole genome sequencing in public health, clinical testing, and forensic laboratories requires the use of validated measurement processes. Well-characterized, homogeneous, and stable microbial genomic reference materials can be used to evaluate measurement processes, improving confidence in microbial whole genome sequencing results. We have developed a reproducible and transparent bioinformatics tool, PEPR, Pipelines for Evaluating Prokaryotic References, for characterizing the reference genome of prokaryotic genomic materials. PEPR evaluates the quality, purity, and homogeneity of the reference material genome, and purity of the genomic material. The quality of the genome is evaluated using high coverage paired-end sequence…

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April 8, 2016

Rapid emergence and evolution of Staphylococcus aureus clones harbouring fusC-containing Staphylococcal cassette chromosome elements.

The prevalence of fusidic acid (FA) resistance amongst Staphylococcus aureus in New Zealand (NZ) is amongst the highest reported globally, with a recent study describing a resistance rate of approximately 28%. Three FA-resistant S. aureus clones (ST5 MRSA, ST1 MSSA and ST1 MRSA) have emerged over the past decade and now predominate in NZ, and in all three clones FA resistance is mediated by the fusC gene. In particular, ST5 MRSA has rapidly become the dominant MRSA clone in NZ, although the origin of FA-resistant ST5 MRSA has not been explored, and the genetic context of fusC in FA-resistant NZ…

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