Genomic profiling of the neonatal meningitic Cronobacter sakazakll clonal complex 4

The Cronobacter sakazakii clonal complex 4 (CC4) represents a dominant lineage of the genus Cronobacter in Cronobacter PubMLST. A strong association of C. sakazakii CC4 with neonatal infections especially neonatal meningitis has been established. The composition of C. sakazakii CC4 isolates in Cronobacter PubMLST indicates that at least 70% of these isolates were obtained either from clinical sources or infant formula. The dominant association of the C. sakazakii CC4 with neonatal infections especially meningitis and its predominant isolation from the infant formula and environment was intriguing which drove the rationale for the in-depth genomic analysis presented in the current PhD study. The whole genome phylogeny revealed that despite their geographical and temporal spread, the CC4 isolates cluster tightly with each other representing a clonal and a stable lineage within the Cronobacter genus. An exhaustive search of the sequenced genomes to identify virulence or environmental fitness associated traits indicated no significant difference between the virulence potential of C. sakazakii CC4 and C. sakazakii non-CC4. The interesting observation was the presence of two hypothetical proteins predominant in CC4 isolates, one of which was the homologue of an inner membrane protein. In addition, an hypothetical protein was noted to be largely absent from the C. sakazakii CC4 genomes. The O:2 was found to be the dominant serotype of CC4, however not exclusive to CC4. A giant adhesion associated gene was also noted predominantly in the C. sakazakii CC4 genomes. Single nucleotide polymorphism indicated low degree of sequence diversity within CC4 with average distance of 300-400 SNPs against the reference isolate. The subdivision of the low invasive CC4 isolates was intriguing, however no unique invasion associated traits were determined in a highly invasive CC4 isolate whereas one low invasive isolate indicated the presence of heavy metal resistance associated traits. The metal resistance assays could not differentiate the high and low invasive CC4 isolates. The case study of the 1994 French outbreak using genome sequenced data suggested powdered infant formula (PIF) to be the dominant, yet not the exclusive source of outbreak for the C. sakazakii isolates. The current PhD study was the first to explore the genomes of C. sakazakii CC4 revealing some interesting variations. Future studies are warranted to characterise hypothetical proteins predominant in CC4 to elucidate their significance in this clonal lineage. Furthermore, transcriptomics studies are warranted to find out any unique genes differentially expressed in the CC4 genomes under different stressful conditions.