Genomic epidemiology of methicillin-resistant Staphylococcus sciuri carrying a SCCmec-mecC hybrid element

Abstract Background Prevention and control of methicillin-resistant Staphylococcus aureus (MRSA) infections remain challenging. In-depth surveillance integrating patient and isolate data can provide evidence to better inform infection control and public health practice. Methods We analyzed MRSA cases diagnosed in 2010 (n = 212) and 2016 (n = 214) by hospitals in Ontario, Canada. Case-level clinical and demographic data were integrated with isolate characteristics, including antimicrobial resistance (AMR), classic genotyping, and whole-genome sequencing results. Results Community-associated MRSA (epidemiologically defined) increased significantly from 23.6% in 2010 to 43.0% in 2016 (P < .001). The MRSA population structure changed over time, with a 1.5× increase in clonal complex (CC)8 strains and a concomitant decrease in CC5. The clonal shift was reflected in AMR patterns, with a decrease in erythromycin (86.7% to 78.4%, P = .036) and clindamycin resistance (84.3% to 47.9%, P < .001) and a >2-fold increase in fusidic acid resistance (9.0% to 22.5%, P < .001). Isolates within both CC5 and CC8 were relatively genetically diverse. We identified 6 small genomic clusters—3 potentially related to transmission in healthcare settings. Conclusions Community-associated MRSA is increasing among hospitalized individuals in Ontario. Clonal shifting from CC5 to CC8 has impacted AMR. We identified a relatively high genetic diversity and limited genomic clustering within these dominant CCs.

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Genomic Epidemiology of Methicillin-Resistant Staphylococcus aureus in a Neonatal Intensive Care Unit

PLoS ONE ◽

10.1371/journal.pone.0164397 ◽

2016 ◽

Vol 11 (10) ◽

pp. e0164397 ◽

Cited By ~ 19

Author(s):

Taj Azarian ◽

Nizar F. Maraqa ◽

Robert L. Cook ◽

Judith A. Johnson ◽

Christine Bailey ◽

...

Keyword(s):

Intensive Care Unit ◽

Staphylococcus Aureus ◽

Intensive Care ◽

Neonatal Intensive Care Unit ◽

Neonatal Intensive Care ◽

Methicillin Resistant Staphylococcus Aureus ◽

Methicillin Resistant ◽

Genomic Epidemiology

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Genomic Epidemiology of USA300 Methicillin-Resistant Staphylococcus aureus in Intensive Care Units (ICUs) Using Whole-Genome Sequencing (WGS)

Open Forum Infectious Diseases ◽

10.1093/ofid/ofw194.128 ◽

2016 ◽

Vol 3 (suppl_1) ◽

Author(s):

Kyle J Popovich ◽

Stefan Green ◽

Koh Okamoto ◽

Yoona Rhee ◽

Mary K. Hayden ◽

...

Keyword(s):

Staphylococcus Aureus ◽

Intensive Care ◽

Whole Genome Sequencing ◽

Intensive Care Units ◽

Genome Sequencing ◽

Methicillin Resistant Staphylococcus Aureus ◽

Whole Genome ◽

Methicillin Resistant ◽

Genomic Epidemiology

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561. Genomic Epidemiology of Methicillin-Resistant Staphylococcus aureus in Two Cohorts of High-Risk Military Trainees

Open Forum Infectious Diseases ◽

10.1093/ofid/ofz360.630 ◽

2019 ◽

Vol 6 (Supplement_2) ◽

pp. S266-S266

Author(s):

Robyn S Lee ◽

Eugene V Millar ◽

Alanna Callendrello ◽

Caroline E English ◽

Alexander E Krasniewski ◽

...

Keyword(s):

Staphylococcus Aureus ◽

High Risk ◽

Methicillin Resistant Staphylococcus Aureus ◽

Phylogenetic Analyses ◽

Control Measures ◽

Pfge Type ◽

High Risk Population ◽

Illumina Hiseq ◽

Methicillin Resistant ◽

Genomic Epidemiology

Abstract Background Methicillin-resistant Staphylococcus aureus (MRSA) skin and soft-tissue infections (SSTIs) are common among military recruits. Identifying which strains are responsible for SSTI and understanding the underlying transmission dynamics is critical to developing appropriate interventions for this high-risk population. Methods A cohort study of US Army Infantry trainees at Fort Benning, GA (June and September 2015). Participants from two training Companies were screened for colonization on multiple anatomic sites throughout the 14-week cycle as well as the time of clinical infection. MRSA+ samples were sequenced with Illumina HiSeq. Multi-locus sequence type (MLST) and virulence genes were identified in silico. Single nucleotide polymorphism (SNP) distances between soldiers’ bacteria were compared with assessing for potential transmission. Results Of 383 soldiers enrolled, 84 (22%) were colonized with MRSA during the study. Forty-two of 84 had a single positive colonization sample, of which 76% were from anatomical sites other than the nares (36% oropharyngeal, 26% perianal, 14% inguinal). Twelve trainees had MRSA SSTI during training (50% had colonization detected prior to or at infection). All were PFGE-type US300 (ST8) and were lukS/lukF-positive. SNP-based phylogenetic analyses and epidemiologic data indicate that most MRSA positives at baseline were due to unique importations from various community origins, suggesting that the ongoing MRSA epidemic is not due to a single endemic strain circulating on base. Following importation, extensive transmission then occurred, with multiple STs implicated. Transmission appeared restricted to within Companies, and predominantly within platoons. Conclusion Frequent colonization at baseline suggests a need for extensive MRSA screening and decolonization upon arrival to base, followed by ongoing infection control measures throughout training to prevent recolonization/infection. As multiple anatomical sites appear to play a role in transmission of MRSA, this may have important implications for screening protocols and control both in community and hospital-based settings. Disclosures All authors: No reported disclosures.

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Genomic Epidemiology of CC30 Methicillin-Resistant Staphylococcus aureus Strains from Argentina Reveals Four Major Clades with Distinctive Genetic Features

mSphere ◽

10.1128/msphere.01297-20 ◽

2021 ◽

Vol 6 (2) ◽

Author(s):

Sabrina Di Gregorio ◽

María Sol Haim ◽

Jesús Vielma Vallenilla ◽

Victoria Cohen ◽

Lucía Rago ◽

...

Keyword(s):

Staphylococcus Aureus ◽

Virulence Genes ◽

Clonal Complex ◽

Sequence Type ◽

Methicillin Resistant ◽

Content Type ◽

Genomic Epidemiology ◽

Type Iv ◽

South West ◽

Chromosomal Mutations

ABSTRACT Staphylococcus aureus clonal complex 30 (CC30) has given rise to epidemics worldwide and is one of the most prevalent lineages in Argentina, represented by sequence type 30 methicillin-resistant S. aureus SCCmec type IV (ST30-MRSA-IV). ST30-MRSA-IV has displaced previous prevalent clones in the country and demonstrated increased virulence. Despite the burden of infections caused by ST30-MRSA-IV both in hospitals and in communities in Argentina, no detailed genome-based characterization of this clone is available to date. In this study, we used whole-genome sequencing (WGS) to evaluate the genetic diversity, population structure, and genomic characteristics of 190 CC30-MRSA strains circulating in Argentina between 2004 and 2015. Phylogenetic analysis revealed the existence of 4 major clades: ARG-1 (CC30-MRSA-IVc-spa t012), ARG-2 (ST30-MRSA-IVc-spa t021 related), ARG-3 (ST30-MRSA-IVh/j-spa t021 and related), and ARG-4 (CC30-MRSA-IVc-spa t019 and related). The clades were characterized by different distributions of antimicrobial resistance determinants, virulence genes, and mobile genetic elements (MGEs). While ARG-1 and ARG-4 were related to global epidemic MRSA-16 (EMRSA-16) and South West Pacific (SWP) clones, respectively, ARG-3 was phylogenetically distinct from previously defined CC30 epidemic clones. ARG-4, the most prevalent and geographically disseminated in the collection (N = 164), was characterized by specific MGEs and chromosomal mutations that might have contributed to its virulence and success. To our knowledge, this is the first genomic epidemiology study of CC30-MRSA in Argentina, which will serve as baseline genomic data going forward to inform public health measures for infection prevention and control. IMPORTANCE The rise in prevalence of community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) is of public health concern. In Argentina, several studies documented a shift in the epidemiology of CA-MRSA since 2009, with clonal complex 30 (CC30) and, in particular, sequence type 30 MRSA SCCmec type IV (ST30-MRSA-IV) replacing other clones both in communities and in hospitals and possibly displaying increased virulence. By sequencing the whole genomes of 190 CC30 MRSA isolates recovered from Argentina between 2005 and 2015, we showed that they represented a diverse population composed of 4 major clades. The predominant clade evolved from the South West Pacific clone but has acquired a distinct repertoire of mobile genetic elements, virulence genes, and chromosomal mutations that might play a role in its success. Our work is the first extensive genomic study of CC30 S. aureus in Argentina and will contribute not only to the development of genomic surveillance in the region but also to our understanding of the global epidemiology of this pathogen.

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