Comparative Genomics of Environmental Multidrug Resistant Staphylococci

Abstract

Multidrug resistant (MDR) staphylococci are public health concern internationally. The treatment of these bacteria have become increasingly difficult due to their resistance to multiple antibiotics. In this thesis, multidrug resistant staphylococci have been recovered from high-frequency touched surfaces in public areas in the community and hospitals in East and West London. In total, 600 isolates collected of which 281 were MDR. In addition, 49 (8.17%) were mecA gene positive (mecA⁺). The most common species identified as multidrug resistant were S. epidermidis, S. haemolyticus and S. hominis, whereas penicillin, fusidic acid and erythromycin were the most frequent antibiotics the isolates were resistant to. Whole genome sequencing (WGS) analysis for mecA+ isolates revealed that among the most frequent antibiotic resistance genes were blaZ, qacA/B and dfrC. Moreover, the mecA⁺ isolates had a diverse range of SCCmec types many of which were untypable due to carrying a novel combination of ccr genes or multiple ccr complexes. mecA⁺ S. epidermidis, S. haemolyticus and S. hominis isolates that have been whole genome sequenced were used in the One Health comparative genomics approach to compare them with isolates obtained from the ENA database that were recovered from clinical samples, healthy human body sites, livestock, companion animals and other environments. The mecA⁺ S. epidermidis and S. haemolyticus isolates in this study were genetically related and shared similar accessory gene profiles with ENA isolates that have been recovered from clinical samples. In addition, all three species mecA⁺ isolates recovered from public settings were genetically related to ENA isolates recovered from different source including healthy humans, livestock, and companion animals, plants and other environmental sources. In conclusion, the high-frequency touched surfaces in public settings are reservoirs for staphylococci belonging to different lineages that are multidrug resistant and therefore pose a potential public health risk.