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Multiplex PCR Assay for Typing of Staphylococcal Cassette Chromosome Mec Types I to V in Methicillin-resistant Staphylococcus aureus
Published on: September 5, 2013
Genomic characterization of two community-acquired methicillin-resistant Staphylococcus aureus with novel sequence
John Njenga1,2,3, Justin Nyasinga1,4,5, Zubair Munshi1
1Department of Pathology, Aga Khan University Hospital, Nairobi, Kenya.
Abstract:
Staphylococcus aureus is a clinically important bacteria with high antimicrobial resistance (AMR) challenge globally. The emergence of methicillin-resistant Staphylococcus aureus (MRSA) clones with unique sequence types have been identified in the community showing evidence that the epidemiology of MRSA globally is changing and requires continual surveillance. We utilized whole genome sequencing to characterize two community acquired-MRSA (CA-MRSA) strains isolated from wound swabs from community-onset infections in two health facilities in Kenya. The two strains belonged to multilocus sequence type (MLST) sequence type (ST) 7460, and ST 7635. The resistance genes detected showed that the novel STs are carriers of clinically relevant resistance genes. Linezolid and mupirocin resistance was observed, yet mupirocin is not commonly used in the country. Mutations within resistance genes were also detected and the pathogenicity toward the human host matched various pathogenic global S. aureus families, e.g., S. aureus subsp. aureus USA300. Multidrug efflux transporters, important in antimicrobial resistance including restriction enzymes type I and type IV were detected. Plasmids identified showed similarities with the plasmids in other clinically significant non-staphylococcal species, such as Pseudomonas aeruginosa, Escherichia coli, Morganella morganii, and Enterococcus faecium. Both STs belong to clonal complex 8 (CC8) which is the most successful MRSA clone in Kenya. Spa type t30 to which ST 7635 belongs has not been reported in the country. The results of this study further highlight the need for epidemiological studies to reveal circulating strains and antimicrobial resistance spread between hospitals and the community. The genomic research highlights resistance to anti-staphylococcal broad-spectrum antimicrobials not used frequently in the country, jeopardizing successful MRSA treatment since most health facilities do not perform genotypic resistance tests for routine patient management. Preliminary insights into unidentified STs of CA-MRSA in Kenya show the need for molecular epidemiological surveillance studies to further understand the diversity of S. aureus in Africa.
Insights
Genomic sequencing revealed novel community-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA) strains in Kenya carrying concerning antimicrobial resistance genes. These findings underscore the urgent need for molecular surveillance to track evolving MRSA epidemiology and resistance patterns in Africa.
Area of Science:
- Genomics and Molecular Epidemiology
- Infectious Diseases and Microbiology
- Antimicrobial Resistance (AMR)
Background:
- Staphylococcus aureus, particularly methicillin-resistant Staphylococcus aureus (MRSA), poses a significant global antimicrobial resistance (AMR) challenge.
- Emerging MRSA clones with unique sequence types (STs) indicate changing global epidemiology, necessitating continuous surveillance.
- Community-acquired MRSA (CA-MRSA) strains are increasingly recognized, highlighting the need to understand their genetic makeup and resistance profiles.
Purpose of the Study:
- To characterize two CA-MRSA strains from community-onset infections in Kenya using whole genome sequencing.
- To identify novel sequence types (STs) and associated antimicrobial resistance genes.
- To understand the genetic relatedness and pathogenic potential of these CA-MRSA strains in the Kenyan context.
Main Methods:
- Whole genome sequencing (WGS) was employed to analyze two CA-MRSA strains isolated from wound swabs.
- Multilocus sequence typing (MLST) was performed to determine the sequence types (STs) of the isolates.
- Analysis included identification of resistance genes, mutations, efflux transporters, and plasmid similarities.
Main Results:
- Two novel CA-MRSA strains were identified, belonging to MLST sequence types ST 7460 and ST 7635, both part of Clonal Complex 8 (CC8).
- These strains carried clinically relevant resistance genes, including resistance to linezolid and mupirocin, and harbored multidrug efflux transporters.
- Identified plasmids showed similarities to those found in other significant bacterial species, and pathogenic profiles matched global MRSA strains like USA300.
Conclusions:
- The study identified novel CA-MRSA STs in Kenya with concerning resistance profiles, including to antimicrobials not commonly used, complicating treatment.
- The findings highlight the need for molecular epidemiological surveillance to track MRSA strain diversity, resistance spread, and inform public health strategies in Africa.
- Genomic insights into these strains emphasize the critical gap in routine genotypic resistance testing in healthcare facilities for effective MRSA patient management.
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