Characterization of methicillin-resistant Staphylococcus aureus through genomics approach

Abstract

In the present study, a total of 35 S. aureus isolates collected from two different geographical locations viz., Germany and Hungary were tested for their methicillin-resistant phenotype which revealed a high incidence of methicillin-resistant S. aureus. The quantitative test for biofilm production revealed that 73.3% of isolates were biofilm producers. The isolates were further characterized using a set of biochemical and genotypic methods such as amplification and analysis of S. aureus species-specific sequence and mecA gene. The 33 mecA positive isolates were then characterized by the amplification of SCCmec and pvl toxin genes. Further, based on the biofilm-forming phenotype, 15 isolates were selected and characterized through PCR–RFLP of coa gene, polymorphism of spa gene and amplification of biofilm-associated genes. The dendrogram prepared from the results of both biochemical and genotypic analyses of the 15 isolates showed that except for the isolates SA G5 and SA H29, the rest of the isolates grouped themselves according to their locations. Thus, the two isolates were selected for further characterization through whole-genome sequencing. Comparative genome analysis revealed that SA G5 and SA H29 have 97.20% ANI values with 2344 gene clusters (core-genome) of which 16 genes were related to antibiotic resistance genes and 57 genes encode virulence factors. The highest numbers of singleton genes were found in SA H29 that encodes proteins for virulence, resistance, mobile elements, and lanthionine biosynthesis. The high-resolution phylogenetic trees generated based on shared proteins and SNPs revealed a clear difference between the two strains and can be useful in distinguishing closely related genomes. The present study demonstrated that the whole-genome sequence analysis technique is required to get a better insight into the MRSA strains which would be helpful in improving diagnostic investigations in real-time to improve patient care.

Genome-wide comparison of four MRSA clinical isolates from Germany and Hungary

“…These genes were detected in all isolates however, the biofilm production ability varies from weak to strong were observed in our previous study ( Naorem et al, 2020 ). Our previous study identified that SA G6 isolate obtained from skin infection showed a weak biofilm-forming ability ( Naorem et al, 2020 ). The low biofilm formation in SA G6 might be degraded the biofilm by DNase enzyme found in skin cells ( Eckhart et al, 2007 ).…”

“…The penicillin resistance gene ( blaZ ) was found absent in SA G8 isolate. This in-silico identification and our previous antibiotic susceptibility test results were correlated with beta-lactam, erythromycin (MLS), and vancomycin antibiotic resistance analysis ( Naorem et al, 2020 ). The secondary metabolite biosynthetic gene clusters identified among the genomes were staphylobactin, aureusimine, bacteriocin, and staphyloferrin A.…”

“…This characterization included antibiotic resistance test (ART), biochemical tests, biofilm-forming assay, and PCR based typing techniques involving the amplification of mecA , pvl , SCCmec -type, spa type, coa-HaeIII -RFLP, and biofilm-associated genes. Principal component analysis from polyphasic characterization data showed that the strains originated from the same geographical region were found in the close group while SA G8, Germany strain was grouped with other Hungarian strains ( Naorem et al, 2020 ). The Hungarian strains (SA H27 and SA H32) belonged to the same Clonal Complex (ST22/ SCCmec -IV) were clustered in the same group; however, these strains were isolated from the different sites of infections (nostrils and trachea) and showed different antibiotic resistance patterns and biofilm-forming abilities.…”

“…The Hungarian strains (SA H27 and SA H32) belonged to the same Clonal Complex (ST22/ SCCmec -IV) were clustered in the same group; however, these strains were isolated from the different sites of infections (nostrils and trachea) and showed different antibiotic resistance patterns and biofilm-forming abilities. Similarly, the strains collected from Germany viz., SA G6, and SA G8 belonged to the same Clonal Complex (ST228/ SCCmec -I and ST225/ SCCmec -II) having similar antibiotic resistance pattern, and biofilm-forming profiles, but these strains were isolated from the different site of infections (skin and other body sites) and not clustered in the same group ( Naorem et al, 2020 ). Based on this information, these four S. aureus strains were chosen for in-depth comparative genome levels study to better understand the genomic differences among the strains.…”

Distinct expression trend of signature antigens of Staphylococcus aureus osteomyelitis correlated with clinical outcomes

“…The S. aureus genome can encode about 2700 proteins, including cytoplasm, cell membrane, cell surface, and secreted proteins 20–22 . Among the many proteins, cell surface and secreted proteins have a high chance of being recognized by the host immune system with resultant antibodies against S. aureus 23–25 . Utilizing a multiantigen Luminex immunoassay with specific antibodies against S. aureus , the humoral immune response can be measured in chronic orthopedic infections and have shown promising value 26–28 .…”