Report of epidemic Pseudomonas aeruginosa AUST-03 (ST 242) strains and
resistomes in South African cystic fibrosis patients
Introduction: Pseudomonas aeruginosa AUST-03 (ST242) has
been reported to cause epidemics in cystic fibrosis (CF) patients from
Tasmania and Australia and has been associated with multidrug resistance
and increased morbidity and mortality. Here, we report epidemic P.
aeruginosa (AUST-03) strains in South African CF patients at a public
academic hospital detected during a previous study and characterise the
resistomes. Methods: The P. aeruginosa AUST-03 (ST242)
strains were analysed with whole genome sequencing using the Illumina
NextSeq2000 platform. Raw sequencing reads were processed using the
Jekesa pipeline and multi-locus sequence typing and resistome
characterisation was performed using public databases. Core single
nucleotide polymorphism phylogenies were performed on P.
aeruginosa ST242 strains from the study and from public databases.
Antibiotic susceptibility testing was performed using the disk diffusion
and broth microdilution techniques. Results: A total of 11
P. aeruginosa AUST-03 strains were isolated from two children
with CF who had pulmonary exacerbations. The majority of the P.
aeruginosa AUST-03 strains (8/11) were multidrug resistant (MDR) or
extensively drug resistant; and the multidrug efflux pumps MexAB-OprM,
MexCD-OprJ, MexEF-OprN, MexXY-OprM were the most clinically relevant
antibiotic resistance determinants and were detected in all of the
strains. The P. aeruginosa AUST-03 (ST242) study strains were
most closely related to strains from Canada, China, Denmark and
Slovenia. Conclusion: Epidemic MDR P. aeruginosa strains
are present at South African public CF clinics and need to be considered
when implementing patient segregation and infection control strategies
to prevent further spread and outbreaks.