Comparing Whole-Genome Sequencing with Sanger Sequencing for
            <i>spa</i>
            Typing of Methicillin-Resistant Staphylococcus aureus

Bartels, Mette Damkjær; Petersen, Andreas; Worning, Peder; Nielsen, Julius; Larner-Svensson, Hanna; Johansen, Helle Krogh; Andersen, Leif Percival; Jarløv, Jens Otto; Boye, Kasper; Larsen, Anders Rhod; Westh, Henrik

doi:10.1128/jcm.01979-14

Cited by 172 publications

(155 citation statements)

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“…Out of the remaining articles, 253 fulfilled our inclusion criteria (Shopsin et al, 1999; Graille et al, 2000; Fey et al, 2003; Arakere et al, 2005; Denis et al, 2005; Ko et al, 2005; Aires-de-Sousa et al, 2006, 2008; Deplano et al, 2006; Durand et al, 2006; Ferry et al, 2006, 2010; Fossum and Bukholm, 2006; Jury et al, 2006; Kuhn et al, 2006; Mellmann et al, 2006, 2008; Montesinos et al, 2006; Ruppitsch et al, 2006, 2007; Sabat et al, 2006; Cai et al, 2007, 2009; Conceicao et al, 2007; Cookson et al, 2007; Ellington et al, 2007a,b; Ghebremedhin et al, 2007; Hallin et al, 2007, 2008; Krasuski et al, 2007; Matussek et al, 2007; Otter et al, 2007; Tristan et al, 2007; Van Loo et al, 2007; Vourli et al, 2007; Werbick et al, 2007; Witte et al, 2007; von Eiff et al, 2007; Bartels et al, 2008, 2013, 2014; Chaberny et al, 2008; Chmelnitsky et al, 2008; Gardella et al, 2008; Fenner et al, 2008a,b; Golding et al, 2008, 2011; Ho et al, 2008a,b, 2012, 2016, 2017; Jappe et al, 2008; Karynski et al, 2008; Larsen et al, 2008, 2009; Nulens et al, 2008; Pérez-Vázquez et al, 2008; Strommenger et al, 2008; Vainio et al, 2008, 2011; Zhang et al, 2008, 2009; Alp et al, 2009; Argudín et al, 2009, 2011; Atkinson et al, 2009; Bekkhoucha et al, 2009; Chen et al, 2009; Chen H.-J. et al, 2010; Chen L. et al, 2010; Chen et al, 20...…”

Section: Resultsmentioning

confidence: 99%

Distribution of the Most Prevalent Spa Types among Clinical Isolates of Methicillin-Resistant and -Susceptible Staphylococcus aureus around the World: A Review

et al. 2018

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Background: Staphylococcus aureus, a leading cause of community-acquired and nosocomial infections, remains a major health problem worldwide. Molecular typing methods, such as spa typing, are vital for the control and, when typing can be made more timely, prevention of S. aureus spread around healthcare settings. The current study aims to review the literature to report the most common clinical spa types around the world, which is important for epidemiological surveys and nosocomial infection control policies.Methods: A search via PubMed, Google Scholar, Web of Science, Embase, the Cochrane library, and Scopus was conducted for original articles reporting the most prevalent spa types among S. aureus isolates. The search terms were “Staphylococcus aureus, spa typing.”Results: The most prevalent spa types were t032, t008 and t002 in Europe; t037 and t002 in Asia; t008, t002, and t242 in America; t037, t084, and t064 in Africa; and t020 in Australia. In Europe, all the isolates related to spa type t032 were MRSA. In addition, spa type t037 in Africa and t037and t437 in Australia also consisted exclusively of MRSA isolates. Given the fact that more than 95% of the papers we studied originated in the past decade there was no option to study the dynamics of regional clone emergence.Conclusion: This review documents the presence of the most prevalent spa types in countries, continents and worldwide and shows big local differences in clonal distribution.

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Section: Resultsmentioning

confidence: 99%

Distribution of the Most Prevalent Spa Types among Clinical Isolates of Methicillin-Resistant and -Susceptible Staphylococcus aureus around the World: A Review

et al. 2018

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“…When amplification was unsuccessful, the PCR was repeated using the alternative primers spa-239f, spa-1717r, spa-1084f, spa-1095f, spa-1618r, and spa-1517r (20, 64). The PCR products were purified (NucleoSpin gel and PCR Clean-Up kit; Macherey and Nagel, Düren, Germany) and sequenced using both amplification primers by a commercial supplier (LGC Genomics GmbH, Berlin, Germany, or GATC, Constance, Germany).…”

Section: Methodsmentioning

confidence: 99%

Molecular Epidemiology of Staphylococcus aureus in the General Population in Northeast Germany: Results of the Study of Health in Pomerania (SHIP-TREND-0)

et al. 2016

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h Population-based studies on Staphylococcus aureus nasal colonization are scarce. We examined the prevalence, resistance, and molecular diversity of S. aureus in the general population in Northeast Germany. Nasal swabs were obtained from 3,891 adults in the large-scale population-based Study of Health in Pomerania (SHIP-TREND). Isolates were characterized using spa genotyping, as well as antibiotic resistance and virulence gene profiling. We observed an S. aureus prevalence of 27.2%. Nasal S. aureus carriage was associated with male sex and inversely correlated with age. Methicillin-resistant S. aureus (MRSA) accounted for 0.95% of the colonizing S. aureus strains. MRSA carriage was associated with frequent visits to hospitals, nursing homes, or retirement homes within the previous 24 months. All MRSA strains were resistant to multiple antibiotics. Most MRSA isolates belonged to the pandemic European hospital-acquired MRSA sequence type 22 (HA-MRSA-ST22) lineage. We also detected one livestock-associated MRSA ST398 (LA-MRSA-ST398) isolate, as well as six livestock-associated methicillin-susceptible S. aureus (LA-MSSA) isolates (clonal complex 1 [CC1], CC97, and CC398). spa typing revealed a diverse but also highly clonal S. aureus population structure. We identified a total of 357 spa types, which were grouped into 30 CCs or sequence types. The major seven CCs (CC30, CC45, CC15, CC8, CC7, CC22, and CC25) included 75% of all isolates. Virulence gene patterns were strongly linked to the clonal background. In conclusion, MSSA and MRSA prevalences and the molecular diversity of S. aureus in Northeast Germany are consistent with those of other European countries. The detection of HA-MRSA and LA-MRSA within the general population indicates possible transmission from hospitals and livestock, respectively, and should be closely monitored.

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“…The spa type was inferred with spaTyper v1.0 15 . The SCCmec type was derived from sequence reads with SRST2 16 and the database available at http://www.staphylococcus.net/Pages/indexEN.html.…”

Section: Bioinformatics Analysismentioning

confidence: 99%

Genomic Surveillance of Methicillin-ResistantStaphylococcus aureusin the Philippines from 2013-2014

Masim

Argimón²,

Espiritu

et al. 2020

Preprint

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Methicillin Resistant Staphylococcus aureus (MRSA) remains one of the leading causes of both nosocomial and community infections worldwide. In the Philippines, MRSA rates have remained above 50% since 2010, but resistance to other antibiotics, including vancomycin, is low. The MRSA burden can be partially attributed to pathogen-specific characteristics of the circulating clones, but little was known about the S. aureus circulating clones in the Philippines.We sequenced the whole genomes of 116 S. aureus isolates collected in 2013-2014 by the Antimicrobial Resistance Surveillance Program. The multi-locus sequence type, spa type, SCC-mec type, presence of antimicrobial resistance (AMR) determinants and virulence genes, and relatedness between the isolates were all derived from the sequence data. The concordance between phenotypic and genotypic resistance was also determined.The MRSA population in the Philippines was composed of a limited number of genetic clones, including several international epidemic clones, such as CC30-spa-t019-SCCmec-IV-PVL+, CC5-SCCmec-typeIV, and ST239-spa-t030-SCCmec-typeIII. The CC30 genomes were related to the South West Pacific clone, but formed a distinct and diverse lineage, with evidence of global dissemination. We showed the independent acquisition of resistance to sulfamethoxazole/trimethoprim across different locations and genetic clones, but mostly in pediatric patients with invasive infections. The concordance between phenotypic and genotypic resistance was 99.68% overall for 8 antibiotics in 7 classes.We produced the first comprehensive genomic survey of S. aureus in the Philippines, which bridges the gap in genomic data from the Western Pacific region and will constitute the genetic background to contextualize ongoing prospective surveillance.

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Comparing Whole-Genome Sequencing with Sanger Sequencing for spa Typing of Methicillin-Resistant Staphylococcus aureus

Cited by 172 publications

References 10 publications

Distribution of the Most Prevalent Spa Types among Clinical Isolates of Methicillin-Resistant and -Susceptible Staphylococcus aureus around the World: A Review

Distribution of the Most Prevalent Spa Types among Clinical Isolates of Methicillin-Resistant and -Susceptible Staphylococcus aureus around the World: A Review

Molecular Epidemiology of Staphylococcus aureus in the General Population in Northeast Germany: Results of the Study of Health in Pomerania (SHIP-TREND-0)

Genomic Surveillance of Methicillin-ResistantStaphylococcus aureusin the Philippines from 2013-2014

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