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Genotypic and Phenotypic Characterization of Cronobacter spp. Strains Isolated from Powdered Milk Formulas and Dairy

Julio Parra-Flores1,2, Beatriz Daza-Prieto3, Miriam Troncoso4

  • 1Department of Nutrition and Public Health, Facultad de Ciencias de la Salud y de los Alimentos, Universidad del Bío-Bío, Chillán 3800708, Chile.

Microorganisms
|March 28, 2026
PubMed

Insights

Cronobacter sakazakii, a pathogen in powdered milk, carries virulence and resistance genes. Genomic analysis revealed multidrug resistance, posing a public health risk requiring strict manufacturing controls.

Area of Science:

  • Food Safety and Microbiology
  • Genomics and Bioinformatics
  • Antimicrobial Resistance

Background:

  • Cronobacter spp. are pathogenic bacteria, with C. sakazakii linked to severe neonatal infections from contaminated powdered infant formula.
  • Virulence factors (VFs) and antibiotic resistance genes (ARGs) contribute to C. sakazakii's pathogenicity and treatment challenges.
  • Next-generation sequencing (NGS) and core genome multilocus sequence typing (cgMLST) offer high-resolution genomic characterization of bacterial strains.

Purpose of the Study:

  • To genomically characterize 34 Cronobacter strains isolated from powdered milk and production environments using cgMLST.
  • To identify specific virulence genes and antibiotic resistance genes present in Cronobacter isolates.
  • To assess the public health implications of multidrug-resistant and virulent Cronobacter strains in dairy products.

Main Methods:

  • Isolation of 34 Cronobacter strains from powdered milk and production surfaces (2011-2022).
  • Genomic characterization using core genome multilocus sequence typing (cgMLST) with a 2831-gene scheme.
  • Detection of virulence genes, antibiotic resistance genes, plasmids, and mobile genetic elements via sequencing.

Main Results:

  • Identified C. sakazakii strains (ST1, ST4, ST13, ST31, ST83) and C. malonaticus (ST60), forming eight distinct clusters.
  • All isolates showed resistance to cephalothin; 18 were resistant to ceftazidime and 11 to ampicillin.
  • Detected various ARGs (e.g., blaCSA, mcr-9.1) and VFs (e.g., cpa, nanAKT), with some genes exclusive to C. sakazakii. All strains harbored plasmids and mobile genetic elements.

Conclusions:

  • The presence of multidrug resistance and virulence genes in Cronobacter isolates from dairy products highlights a significant public health concern.
  • Genomic surveillance using cgMLST is crucial for understanding strain diversity and tracking the spread of Cronobacter.
  • Implementation of stringent hygienic manufacturing practices and Hazard Analysis and Critical Control Points (HACCP) is essential to mitigate risks associated with C. sakazakii contamination.

Keywords:
Cronobacter malonaticusCronobacter sakazakiiWGSdairy production environmentpowdered milk

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