Comparative genomics of Cronobacter sakazakii strains from a powdered infant formula plant reveals evolving populations
Marc J. A. Stevens, Nicole Cernela, Roger Stephan, Angelika Lehner
Abstract
Cronobacter sakazakii is an opportunistic pathogen causing life-threatening infections in newborns. C. sakazakii strains (N = 26) isolated from a powdered infant formula (PIF) plant over a 15-years period were sequenced. Seventeen strains belonged to sequence type ST83 and nine to ST4. Core-genome MLST revealed clonality of most ST83 and some ST4 strains, showing that these stains derive from persistent populations. A genome comparison between the ST83 and ST4 strains identified population-specific genes, of which some are potentially involved in persistence, such as aggregation and stress-resistance genes in ST83 and fimbrial genes in ST4 strains. A single nucleotide polymorphisms comparison revealed 20 SNPs in a lactose operon. This lactose operon was shown to be transposon associated and was present in all PIF isolates, yet only in 171 of 449 public available C. sakazakii genomes, suggesting a role for lactose as evolutionary force in a PIF environment. Eighteen and 20 antimicrobial resistance genes were found in the ST83 and ST4 strain set, respectively. Four ST4 strains possessed a mcr6.1 gene acquired via HGT. encoding colistin resistance. We show that evolving C. sakazakii populations persist concomitantly in an industrial environment, which has a potential impact on public health.