Escherichia coli (E. coli) is an important pathogenic bacterium that needs to be monitored in the powdered infant formula (PIF) processing environment, and its acid resistance may compromise the cleaning effect, leading to an increase in the prevalence rate. In this study, 56 E. coli strains were isolated from 1,130 samples collected in 8 PIF factories, and strains were classified into 19 STs. The strain EC56 with the strongest acid resistance was selected for transcriptome and proteome sequencing. The correlation analysis results indicated that EC56 mainly enhanced acid resistance through the regulation of two systems: glutamate-dependent acid-tolerance (Gad) and ornithine dependent acid-tolerant (Orn). In addition, the expression of acid shock protein (asr gene), which can prevent cell inactivation under acid stress, and DNA protection during starvation protein (dps gene), which can bind to DNA and protect DNA from acid-induced strand breaks, was significantly upregulated. The downregulation of the OmpF (ompF gene) and tryptophanase (tnaA gene) also enhanced the acid resistance of bacteria. Fortunately, the expression levels of most virulence factors of E. coli, especially those related to motility function, were significantly downregulated after acid stress. This study reveals the molecular regulatory mechanism to acid stress and the changes in virulence factors of E. coli in the PIF processing environment, which is helpful for production enterprises to carry out hazard prevention and control and predict the changes in bacterial pathogenicity.

Cronobacter spp. has strong resistance to desiccation and high permeability in Enterobacteriaceae, and powdered infant formula (PIF) is one of the main contamination routes. In recent years, the contamination of Cronobacter spp. in PIF incidents occurs from time to time, causing infant serious diseases or death. In this investigation, matrix-assisted laser desorption/ionization time of flight mass spectrometry was used to identify the phenotypes of 35 Cronobacter strains isolated from PIF and its processing environment. Subsequently, the isolates were evaluated for drying and osmotic pressure tolerance. The results showed that the deactivation rate of the strains ranged from 9.01% to 77.57%, and the highest osmotic pressure condition the strains could tolerate was 6 g/100 mL NaCl. In addition, there was a positive correlation between biofilm formation ability and desiccation resistance. Combined with transcriptomics, Cronobacter spp. could activate biofilm synthesis, produce more trehalose, accumulate betaine and electrolytes to stabilize intracellular structure under the two treatment conditions. A total of 31 and 43 genes were found related to desiccation and permeability resistance, respectively. And some genes (cysM, thuF, ycjO, etc.) were found to be associated with two tolerances for the first time.