LAUSR

OBJECTIVES The underlying resistance mechanism and phylogenetic relationship of a colistin-resistant Salmonella Enteritidis strain EC20120916 that resulted in fatal meningitis in an immune-compromised patient was investigated by analysing the genome sequence. METHODS Whole-genome sequencing was performed on strain EC20120916 with the Illumina MiSeq platform. Annotation of the sequence was performed using the prokaryotic genome annotation pipeline (PGAP). Antibiotic resistance gene, plasmid replicons and pathogenicity islands were identified. A phylogenetic tree was constructed using Parsnp and edited with Figtree. RESULTS The genome size was 4, 699, 318 bp with a GC content of 55.2% and 4471 protein-encoding genes. The aac(6')-laa gene, encoding resistance to aminoglycosides, was identified, although this was not expressed phenotypically in the isolate. No colistin resistance-conferring mutations or plasmid-mediated mechanisms were identified to explain the colistin resistance. The strain was phylogenetically related to three international strains, although it was not close enough to suggest importation from outside South Africa. CONCLUSION This is the first report of a colistin-resistant Salmonella Enteritidis isolate causing meningitis in an immune-compromised patient in South Africa. The absence of colistin resistance-conferring mutations or plasmid-mediated resistance mechanisms suggest that a novel mechanism is responsible for the colistin resistance in this isolate. The isolate was acquired locally.