Objective: To determine molecular epidemiology of Methicillin-resistant S. aureus in Tanzania using locally available whole genome sequencing tools.

Methods: DNA from 30 S. aureus strains and three coagulase negative staphylococcus (CoNS) were recovered upon subculturing of archived Staphylococcus isolates. Whole genome sequencing (WGS) of the library was performed on Illumina Miseq using paired-end 2x250 bp protocol. Raw sequence data were analyzed using online tools available at Center for Genomic Epidemiology (CGE) (https://cge.cbs.dtu.dk/services/). Additional 34 genome sequences were obtained from the ENA (http://www.ebi.ac.uk/ena) and NCBI for phylogenetic comparison.

Results: Full susceptibility to vancomycin and chloramphenicol was observed. Thirteen isolates (43.3%) were resistant to cefoxitin and other antimicrobials tested. Multilocus sequence typing revealed 13 different sequence types (ST) among the 30 S. aureus isolates, with ST-8 (n=seven, 23%) being the most common. Gene detection in S.aureus stains was as follows; mecA 10 (33.3%), pvl 5 (16.7%) and 2 (6.7%) tst . The SNP difference among the six Tanzanian ST-8 MRSA isolates ranged from 24 to 196 SNPs and from 16 to 446 SNPs when using the USA300_FPR3757 or the USA500_2395 as a reference, respectively. The mutation rate was 1.38x10-11 SNPs/site/year or 1.4x10-6 SNPs/site/year as estimated by USA300_FPR3757 or the USA500_2395 respectively.

Conclusion: S. aureus causing infections in hospitalized patients in Moshi are highly diverse and epidemiologically unrelated. Temporal phylogenetic analysis provided better resolution on transmission and introduction of MRSA and it may be important to include this in future routines.