Genomic Epidemiology of Cronobacter spp. in Ready-to-Eat Boxed Meals: High Prevalence, Virulence, and Cefazolin Resistance in Nanning, China.

Cronobacter spp. cause severe neonatal meningitis and sepsis with a case-fatality rate exceeding 40%, yet ready-to-eat (RTE) boxed meals, an emerging transmission vehicle, remain unassessed for food protection. This study investigated the prevalence, genomic characteristics, and antimicrobial resistance of Cronobacter spp. in RTE boxed meals in Nanning, China. Among 117 samples, 14 (11.97%) were positive for Cronobacter, including Cronobacter sakazakii (n = 11), C. malonaticus (n = 2), and C. dublinensis (n = 1). Fourteen isolates representing eight serotypes were identified, including one O-antigen gene cluster-deficient strain of C. sakazakii, which represents the first report of such a deficiency in RTE food isolates. Multilocus sequence typing revealed nine sequence types, with ST4 and ST8, both associated with neonatal meningitis outbreaks, as the most common. Clustering and phylogenetic analysis of 3,157 single-copy orthogroups revealed that the 14 isolates share a highly conserved genomic composition. Heat tolerance genes were highly prevalent: hsp31 (14/14, 100%), shsp20 (10/14, 71.4%), and clpK1 (10/14, 71.4%). A total of 92.9% of isolates were resistant to cefazolin, and two exhibited multidrug resistance. Notably, heat tolerance genes including clpK1 were frequently colocated with resistance determinants on mobile genetic elements. The presence of clinically significant sequence types (ST4, ST8) and heat tolerance virulence factors in RTE boxed meals underscores a potential public health risk for noninfant populations. These findings highlight the need for routine surveillance of RTE prepared meals and specific attention to postprocessing contamination.