Cronobacter sakazakii 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 Cronobacter strains from the contaminated products. Seven strains were identified as C. sakazakii, and the remaining strain was Franconibacter helveticus. All C. sakazakii strains adhered to a neuroblastoma cell line, and 31 virulence genes were predicted by WGS. The antibiograms varied between strains. and included mcr-9.1 and bla CSA genes, conferring resistance to colistin and cephalothin, respectively. The C. sakazakii 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 C. sakazakii 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.

Austrian Agency for Health and Food Safety Institute for Medical Microbiology and Hygiene Vienna Austria

Department of Nutrition and Public Health Universidad del Bío Bío Chillán Chile

Department of Public Health Palacký University Olomouc Olomouc Czechia

Faculty of Medicine Biological Sciences Graduate Program Posgrado en Ciencias Biológicas Universidad Nacional Autónoma de México Mexico City Mexico

foodmicrobe com Nottinghamshire United Kingdom

Intestinal Bacteriology Research Laboratory Hospital Infantil de México Federico Gómez Mexico City Mexico

Microbiology and Probiotics Laboratory Institute of Nutrition and Food Technology Universidad de Chile Santiago Chile

Servicio de Salud Ñuble Chillán Chile

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Screening of Antibiotic and Virulence Genes from Whole Genome Sequenced Cronobacter sakazakii Isolated from Food and Milk-Producing Environments

Genomic Characterization of Cronobacter spp. and Salmonella spp. Strains Isolated From Powdered Infant Formula in Chile