Mechanisms of acid resistance and changes in virulence factors of <em>Escherichia coli</em> isolated from powdered infant formula processing environment based on transcriptome and proteome analysis

<em>Escherichia coli</em><em> </em>(<em>E. coli</em>) 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 <em>E. coli </em>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 (<em>asr</em> gene), which can prevent cell inactivation under acid stress, and DNA protection during starvation protein (<em>dps</em> gene), which can bind to DNA and protect DNA from acid-induced strand breaks, was significantly upregulated. The downregulation of the OmpF (<em>ompF</em> gene) and tryptophanase (<em>tnaA</em> gene) also enhanced the acid resistance of bacteria. Fortunately, the expression levels of most virulence factors of <em>E. coli</em>, 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 <em>E. coli</em> 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.