Browsing by Author "Kaipainen, Suvi"

In this study 39 methicillin-resistant Staphylococcus aureus CC398 isolates from Finnish pigs and pork were sequenced by whole-genome sequencing. Also, phenotypic antimicrobial resistance of the strains was examined. The strains originated from the culture collection of Finnish Food Safety Authority (Evira) and they were isolated between the years of 2008 and 2017. MRSA strains were isolated from both asymptomatic and infected pigs and pork. The strains represented the four most common spa types in Finnish pigs (t034, t2741, t011 and t108). DNA extraction method for S. aureus was optimized by comparing automatic DNA extraction robot and manual DNA extraction method. Extracted DNA samples were sent to Germany to be sequenced with Illumina sequencing. Paired-end raw read sequences were assembled using three different algorithms: Spades, Idba and Velvet. The assembled sequences were analysed by bioinformatics tools. Possible antimicrobial resistance genes, virulence genes, plasmids and SCCmec cassettes were identified. The strains were also typed by spa typing and sequence typing. spa typing was already performed in Evira using PCR and the new spa typing results were compared to the PCR results. Using the assembled sequences, a phylogenetic tree was also constructed. Phenotypic antimicrobial susceptibility testing was performed using broth microdilution panel. The manual extraction method was slightly better since the extracted DNA was purer. The best assembly algorithm was Spades and because of that all sequences were assembled with that algorithm for further analyses. The strains carried only a few virulence genes and many genes that are important for human infection were missing. All the strains carried the same SCCmec cassette type and sequence type ST398 both of which are known to be typical for pig related MRSA. Illumina sequencing and spa typing were not working perfectly since the used program was not able to distinguish spa types t034 and t011 from each other. The problem was probably due to very similar short tandem repeats that these two spa types share. Also, Illumina sequencing is known to produce short reads that could be problematic for sequence assembly. All the strains were resistant to beta-lactams and tetracycline which is typical for MRSA CC398 strains. Many strains were also resistant to clindamycin and trimethoprim. Antimicrobial resistance seemed to be carried by plasmids in some cases because the strains carried several plasmids that are known to contain antimicrobial resistance genes. The antimicrobial resistance profiles were different between different spa types since some spa types were more resistant to certain antimicrobials than others. According to the phylogenetic tree, the strains seemed to be a very heterogenic group. The strains that belonged in the same spa type were most related to each other as expected. There were no differences between strains originating from pigs and strains originating from pork which strongly indicates that bacteria could have spread from pigs to pork. Asymptomatic pigs also carried similar strains as infected pigs. The strains that were causing infections in pigs did not contain any more virulence factors compared to the other strains. The study gave plenty of new information concerning MRSA CC398 in Finnish pigs and pork. The antimicrobial resistance and virulence patterns in addition to other qualities of the strains were very similar that was described in the literature before. The strains seemed not to be very virulent for humans, but the situation must be observed in case of increasing resistance and virulence. The best way to prevent spreading of MRSA is to decrease the amount of MRSA in pig farms since MRSA bacteria are most likely to spread from pigs to the environment and to the people who work in pig farms and from there to the rest of the population.