Molecular characterisation of Pseudomonas aeruginosa isolated from Otitis externa in Sodwana Bay

Abstract: Pseudomonas aeruginosa (P. aeruginosa) in relation to otitis externa infections were isolated from different sources in Sodwana Bay, South Africa. The isolates were tested against a selection of antibiotics and characterised using molecular biology techniques. To identify the isolates, their 16S rRNA was sequenced and compared to the sequences present on NCBI. After the confirmation of the identity of the isolates as P. aeruginosa, the disk diffusion test was done using antibiotics such as Meropenem, Bactrim, Augmentin, Penicillin, Clarithromycin, Amikacin and Ciprofloxacin. This was followed by the detection of resistance genes TEM, OXA, ampC, SHV, sul1, sul2 and sul3; as well as the integrons intL1 and intL2 via PCR. MLST was further performed on the isolates through the amplification and sequencing of the seven housekeeping genes acsA, aroE, guaA, mutL, nuoD, ppsA and trpE. The housekeeping genes of each isolates were concatenated. Phylogenetic trees were built using the sequences obtained. A great majority (with the percentage ranging from 100 to 82%) of the isolates were found to be resistant to Bactrim, Augmentin, Penicillin, Clarithromycin but sensitive to Amikacin, Ciprofloxacin and Meropenem. The resistance gene ampC was the most (91%) detected in the isolates whilst sul3 was the gene that was the least (4.35%) detected. Ten different allelic profiles corresponding to sequence types present in the pubmlst repository were identified with the most recurrences being ST316 with two occurrences and the isolate corresponding to ST253 which corresponds to PA14 a P.aeruginosa clonal complex rich with multidrug resistant isolates. New sequence type numbers were assigned to the isolates with novel allelic profiles by the curator of the P. aeruginosa pubmlst database. The Pseudomonas isolates from Sodwana bay showed a great diversity with varying susceptibility profiles, however, Meropenem, ciprofloxacin and amikacin could be used against P. aeruginosa from Sodwana Bay. Some displayed similitudes in terms of allelic profiles with numerous globally isolated Pseudomonas aeruginosa species.M.Sc. (Biotechnology