Profiling the Virulence and Antibiotic Resistance Genes of Cronobacter sakazakii Strains Isolated From Powdered and Dairy Formulas by Whole-Genome Sequencing

Abstract

<i>Cronobacter sakazakii</i> is an enteropathogen that causes neonatal meningitis, septicemia, and necrotizing enterocolitis in preterm infants and newborns with a mortality rate of 15 to 80%. Powdered and dairy formulas (P-DF) have been implicated as major transmission vehicles and subsequently the presence of this pathogen in P-DF led to product recalls in Chile in 2017. The objective of this study was to use whole genome sequencing (WGS) and laboratory studies to characterize <i>Cronobacter</i> strains from the contaminated products. Seven strains were identified as <i>C. sakazakii</i>, and the remaining strain was <i>Franconibacter helveticus</i>. All <i>C. sakazakii</i> strains adhered to a neuroblastoma cell line, and 31 virulence genes were predicted by WGS. The antibiograms varied between strains. and included <i>mcr-9.1</i> and <i>bla</i> _<i>CSA</i> genes, conferring resistance to colistin and cephalothin, respectively. The <i>C. sakazakii</i> strains encoded I-E and I-F CRISPR-Cas systems, and carried IncFII(pECLA), Col440I, and Col(pHHAD28) plasmids. In summary, WGS enabled the identification of <i>C. sakazakii</i> strains and revealed multiple antibiotic resistance and virulence genes. These findings support the decision to recall the contaminated powdered and dairy formulas from the Chilean market in 2017.