Diverse Genotypes of <i>Cronobacter</i> spp. Associated with Dairy Farm Systems in Jiangsu and Shandong Provinces in China

<i>Cronobacter</i> spp. are the most concerning foodborne pathogen in infant formula milk powder. Currently, there are many reports on the prevalence of <i>Cronobacter</i> spp. in infant formula milk and its processing environment, but there are few studies on the prevalence of <i>Cronobacter</i> spp. on dairy farms. We have, therefore, undertaken this study to investigate and track genomic epidemiology of <i>Cronobacter</i> spp. isolates from Chinese dairy farms in the provinces of Jiangsu and Shandong. In this study, forty <i>Cronobacter</i> spp. strains, consisting of thirty <i>Cronobacter sakazakii</i>, eight <i>Cronobacter malonaticus</i>, and two <i>Cronobacter dublinensis</i>, were obtained from 1115 dairy farm samples (raw milk, silage, bedding, and feces), with a prevalence rate of 3.57%. These isolates were classified into 10 <i>Cronobacter</i> serotypes and 31 sequence types (STs), including three novel STs which were isolated for the first time. Notably, pathogenic <i>Cronobacter</i> STs 7, 8, 17, 60, and 64, which are associated with clinical infections, were observed. Antimicrobial susceptibility testing showed that all the <i>Cronobacter</i> spp. were highly resistant to cephalothin and fosfomycin, which was consistent with the antimicrobial genotype. All isolates carried core virulence genes related to adherence, invasion, endotoxin, immune evasion, secretion system, and regulation. Approximately half the isolates were also able to produce a strong biofilm. Twenty-one prophages and eight plasmids were detected, with the most common prophage being <i>Cronobacter</i>_ENT47670 and the most common plasmid being IncFIB (pCTU1). In addition, two isolates harbored the transmissible locus of stress tolerance (tLST) which confers high environmental persistence. Phylogenetic analysis showed strong clustering by species level and sequence types. Isolates from different sources or regions with a similar genomic background suggests the cross-contamination of <i>Cronobacter</i> spp. The presence of diverse genotypes of <i>Cronobacter</i> spp. in dairy farms in Jiangsu and Shandong provinces indicates that surveillance of <i>Cronobacter</i> spp. on dairy farms should be strengthened, to prevent and control transmission and ensure the quality and safety of raw dairy products.