Large-scale genomic survey and characterization of mcr genes carried by foodborne Cronobacter isolates

Antibiotic resistance has become a worldwide public health and biosafety problem. The clinical efficacy of colistin was jeopardized by the report of the first mobile colistin resistance (mcr) gene, and subsequently, the mcr-gene family of mcr-1 to mcr-10 has been identified. Cronobacter is an emerging foodborne opportunistic pathogen, which can cause neonatal meningitis, bacteremia, and necrotizing enterocolitis (NEC) by contaminating food. However, the entire picture of foodborne Cronobacter carriage of the mcr genes is not known. Here, we investigated the mcr genes of Cronobacter isolates (N = 877) by whole-genome sequencing. We found 133 of 877 previously undescribed Cronobacter isolates carrying mcr genes. Further genomic analysis revealed that these mcr genes mainly belonged to the mcr-9 and mcr-10. Genomic analysis of the flanking structures of mcr genes revealed that two core flanking structures were prevalent in foodborne Cronobacter isolates, and the flanking structure carrying IS1R was found for the first time in this study. These findings suggest that foodborne Cronobacter isolates carrying the mcr genes already pose a threat to human health. IMPORTANCE Cronobacter is an emerging foodborne opportunistic pathogen, which can cause neonatal meningitis, bacteremia, and NEC by contaminating food. However, the entire picture of foodborne Cronobacter carriage of the mcr genes is not known. Here, we investigated the mcr genes of Cronobacter isolates by whole-genome sequencing and found 133 previously undescribed Cronobacter isolates carrying mcr genes. Further genomic analysis revealed that these mcr genes mainly belonged to the mcr-9 and mcr-10. Genomic analysis of the flanking structures of mcr genes revealed that two core flanking structures were prevalent in foodborne Cronobacter isolates, and the flanking structure carrying IS1R was found for the first time in this study.