RNA Sequencing Based Transcriptional Overview of Xerotolerance in Cronobacter sakazakii SP291.

Cronobacter sakazakii is a xerotolerant neonatal pathogen epidemiologically linked to powdered infant food formula, often resulting in high mortality rates. Here, we used RNA-seq to provide transcriptional insights into the survival of C. sakazakii in desiccated conditions. Our RNA-seq data shows that about 22% of the total C. sakazakii genes were significantly up-regulated and 9% were down-regulated during desiccation survival. When qRT-PCR was used to validate the RNA-seq data, we found that the primary desiccation response was gradually down-regulated during the tested four hours of desiccation while the secondary response remained constitutively up-regulated. The 4-hour desiccation tolerance of C. sakazakii was dependent on the immediate microenvironment surrounding the bacterial cell. Removal of TSB salts and the introduction of sterile infant formula residues in the microenvironment enhanced the desiccation survival of C. sakazakii SP291. The trehalose biosynthetic pathway encoded by otsA and otsB , a prominent secondary bacterial desiccation response, was highly up-regulated in desiccated C. sakazakii C. sakazakii SP291 Δ otsAB was significantly inhibited compared to the isogenic wild type in an eight hour desiccation survival assay confirming the physiological importance of trehalose in desiccation survival. Overall, we provide a comprehensive RNA-seq based transcriptional overview along with confirmation of the phenotypic importance of trehalose metabolism in Cronobacter sakazakii during desiccation. IMPORTANCE Cronobacter sakazakii is a pathogen of importance to neonatal health that is known to persist in dry food matrices such as powdered infant formula (PIF) and its associated production environment. When infections are reported in neonates, mortality rates can be high. The success of this bacterium in surviving these low-moisture environments suggests that Cronobacter species can respond to a variety of environmental signals. Therefore, understanding those signals that aid persistence of this pathogen in these ecological niches, is an important step towards the development of strategies to reduce the risk of contamination of PIF. This research led to the identification of candidate genes that play a role in the persistence of this pathogen in desiccated conditions and, thereby, serve as a model target to design future strategies to mitigate PIF associated survival of C. sakazakii .