Insights into the genomic features of the emerging pathogens Cronobacter malonaticus and Cronobacter turicensis

Cronobacter spp. are emerging opportunistic bacteria that are able to survive to diverse stresses. They infect mainly children through contaminated food. Despite the growing concern surrounding them, Cronobacter malonaticus (C. malonaticus) and Cronobacter turicensis (C. turicensis) remain understudied. This study aimed to characterize the genomic traits of C. malonaticus and C. turicensis isolated worldwide. A total of 104 C. malonaticus and 89 C. turicensis genomes from eight countries and diverse sources were screened for antimicrobial resistance and virulence genes, plasmids, and prophages. Genotyping was performed by Multi-Locus Sequence Typing (MLST), core-genome MLST, and Single-Nucleotide Polymorphism (SNP) clusters. Only six C. malonaticus genomes harbored resistance genes, while all C. turicensis genomes harbored the fosfomycin resistance gene fos. The IncFIB(pCTU1) and IncFIB(pCTU3) plasmid replicons and the prophage 118970_sal3 were the most frequent. Seventy-one virulence genes related to chemotaxis, flagella, hemolysins, intra-macrophage survival, outer membrane proteins, stress response and transcriptional regulation were found in all genomes. All molecular typing methods suggested a high intra-species genomic diversity, regardless of the isolation source or country. In conclusion, the high frequency of virulence genes in C. malonaticus and C. turicensis suggests their pathogenic potential and capacity to cause infection in humans, reinforcing the need to not underestimate the potential hazard of understudied Cronobacter species. The high genetic diversity, the presence of certain antimicrobial resistance genes, and the variety of plasmids and prophages reinforce the importance of monitoring C. malonaticus and C. turicensis worldwide by public health and food safety authorities.