SCC
            <i>mec</i>
            Finder, a Web-Based Tool for Typing of Staphylococcal Cassette Chromosome
            <i>mec</i>
            in Staphylococcus aureus Using Whole-Genome Sequence Data

Kaya, Hülya; Hasman, Henrik; Larsen, Jesper; Stegger, Marc; Johannesen, Thor Bech; Allesøe, Rosa Lundbye; Lemvigh, Camilla K.; Aarestrup, Frank Møller; Lund, Ole; Larsen, Anders Rhod

doi:10.1128/msphere.00612-17

Cited by 232 publications

(200 citation statements)

References 13 publications

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“…Acquired resistance genes were identified and multilocus sequence types where extracted from the genome sequence using ResFinder‐3.1 (Zankari et al ) and mlst 2.0 (Larsen et al ) respectively. spa ‐typing and SCC mec typing from the genome sequences was performed by SCC mec Finder 1.2 (Kaya et al ) and spaTyper 1.0 (Bartels et al ) respectively.…”

Section: Methodsmentioning

confidence: 99%

Low prevalence of livestock‐associated methicillin‐resistantStaphylococcus aureusclonal complex 398 andmecCMRSA among human isolates in North‐West England

Paterson

2020

J Appl Microbiol

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Aims Livestock‐associated methicillin‐resistant Staphylococcus aureus (LA‐MRSA) is an important public health problem in many countries. Despite reports of such isolates being found in both animals and humans in the United Kingdom few data are available on the prevalence in humans of such isolates. A prevalence study was therefore undertaken in the north‐west of England. Methods and Results One thousand two hundred and forty‐two human MRSA isolates collected during 2015 were screened by PCR to detect two of the major forms of LA‐MRSA: clonal complex (CC)398 and mecC MRSA. Isolates identified were further characterized by antimicrobial susceptibility testing and whole‐genome sequencing using HiSeq technology. A single mecC MRSA isolate and three CC398 LA‐MRSA were identified among the isolates screened. All four isolates were from MRSA screening. A phylogenetic analysis, including previously sequenced isolates from the United Kingdom, provided strong evidence for the genomic and epidemiological linkage between a pair of animal and human isolates of CC398 LA‐MRSA in England. These data are indicative of animal and humans isolates of CC398 LA‐MRSA being involved in the same transmission network and is the first demonstration of such closely linked animal and human isolates of this lineage in the UK. Conclusions The study indicates there is a low prevalence of CC398 LA‐MRSA and mecC MRSA among MRSA isolates in the sampled population. Significance and Impact of the Study While the study demonstrates that LA‐MRSA were rare among human MRSA isolates in the sampled population, the data provide a baseline for the future surveillance of what is a significant public health challenge in some regions. The demonstration of linked human and animal isolates of CC398 LA‐MRSA, supported by genomic and epidemiological data, reinforces the need for such surveillance and for continued awareness of the risks that LA‐MRSA may pose in the UK.

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Section: Methodsmentioning

confidence: 99%

Low prevalence of livestock‐associated methicillin‐resistantStaphylococcus aureusclonal complex 398 andmecCMRSA among human isolates in North‐West England

Paterson

2020

J Appl Microbiol

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“…8) (455). Recently, based on the structural diversity described above, a new online tool (SCCmecFinder; https://cge.cbs.dtu.dk/services/SCCmecFinder) was developed for rapid, sequence-based SCCmec typing of MRSA (466).…”

Section: (See Below)mentioning

confidence: 99%

Mobile Genetic Elements Associated with Antimicrobial Resistance

et al. 2018

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SUMMARYStrains of bacteria resistant to antibiotics, particularly those that are multiresistant, are an increasing major health care problem around the world. It is now abundantly clear that both Gram-negative and Gram-positive bacteria are able to meet the evolutionary challenge of combating antimicrobial chemotherapy, often by acquiring preexisting resistance determinants from the bacterial gene pool. This is achieved through the concerted activities of mobile genetic elements able to move within or between DNA molecules, which include insertion sequences, transposons, and gene cassettes/integrons, and those that are able to transfer between bacterial cells, such as plasmids and integrative conjugative elements. Together these elements play a central role in facilitating horizontal genetic exchange and therefore promote the acquisition and spread of resistance genes. This review aims to outline the characteristics of the major types of mobile genetic elements involved in acquisition and spread of antibiotic resistance in both Gram-negative and Gram-positive bacteria, focusing on the so-called ESKAPEE group of organisms (, ,, ,, spp., and), which have become the most problematic hospital pathogens.

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“…The SCCmec type and its structural composition in the MRSA isolates were determined in-silico using the web-based tool SCCmecFinder, freely available at https://cge.cbs.dtu.dk/services/ SCCmecFinder [98]. Spa typing of MRSA isolates was performed in-silico using the assembled genomic sequences on the online platform tool Spa Typer 1.0 [99].…”

Section: Wgs-based Molecular Typing Of the Obtained Mrsamentioning

confidence: 99%

Genome Mining and Comparative Pathogenomic Analysis of An Endemic Methicillin-Resistant Staphylococcus Aureus (MRSA) Clone, ST612-CC8-t1257-SCCmec_IVd(2B), Isolated in South Africa

et al. 2019

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This study undertook genome mining and comparative genomics to gain genetic insights into the dominance of the methicillin-resistant Staphylococcus aureus (MRSA) endemic clone ST612-CC8-t1257-SCCmec_IVd(2B), obtained from the poultry food chain in South Africa. Functional annotation of the genome revealed a vast array of similar central metabolic, cellular and biochemical networks within the endemic clone crucial for its survival in the microbial community. In-silico analysis of the clone revealed the possession of uniform defense systems, restriction-modification system (type I and IV), accessory gene regulator (type I), arginine catabolic mobile element (type II), and type 1 clustered, regularly interspaced, short palindromic repeat (CRISPR)Cas array (N = 7 ± 1), which offer protection against exogenous attacks. The estimated pathogenic potential predicted a higher probability (average Pscore ≈ 0.927) of the clone being pathogenic to its host. The clone carried a battery of putative virulence determinants whose expression are critical for establishing infection. However, there was a slight difference in their possession of adherence factors (biofilm operon system) and toxins (hemolysins and enterotoxins). Further analysis revealed a conserved environmental tolerance and persistence mechanisms related to stress (oxidative and osmotic), heat shock, sporulation, bacteriocins, and detoxification, which enable it to withstand lethal threats and contribute to its success in diverse ecological niches. Phylogenomic analysis with close sister lineages revealed that the clone was closely related to the MRSA isolate SHV713 from Australia. The results of this bioinformatic analysis provide valuable insights into the biology of this endemic clone.

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SCC mec Finder, a Web-Based Tool for Typing of Staphylococcal Cassette Chromosome mec in Staphylococcus aureus Using Whole-Genome Sequence Data

Cited by 232 publications

References 13 publications

Low prevalence of livestock‐associated methicillin‐resistantStaphylococcus aureusclonal complex 398 andmecCMRSA among human isolates in North‐West England

Low prevalence of livestock‐associated methicillin‐resistantStaphylococcus aureusclonal complex 398 andmecCMRSA among human isolates in North‐West England

Mobile Genetic Elements Associated with Antimicrobial Resistance

Genome Mining and Comparative Pathogenomic Analysis of An Endemic Methicillin-Resistant Staphylococcus Aureus (MRSA) Clone, ST612-CC8-t1257-SCCmec_IVd(2B), Isolated in South Africa

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