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Core genome and whole genome multi-locus sequence typing of Cronobacter isolates

Lavin A Joseph1, Krittika Krishnan1,2, Cynney Walters1,3

  • 1Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.

Microbiology Spectrum
|August 10, 2026
PubMed

Insights

Whole genome sequencing (WGS) methods like core genome MLST (cgMLST) and whole genome MLST (wgMLST) effectively subtype Cronobacter isolates. These WGS approaches enhance Cronobacter outbreak detection and public health response strategies.

Area of Science:

  • Food safety and public health microbiology
  • Genomic epidemiology
  • Infectious disease surveillance

Background:

  • Cronobacter species, particularly C. sakazakii and C. malonaticus, are opportunistic pathogens causing severe infant infections with high mortality.
  • Advanced molecular subtyping is crucial for effective public health surveillance of Cronobacter.

Purpose of the Study:

  • To investigate and validate whole genome sequencing (WGS) analysis approaches for subtyping Cronobacter isolates.
  • To assess the utility of 7-gene MLST, core genome MLST (cgMLST), and whole genome MLST (wgMLST) for Cronobacter surveillance.
  • To evaluate WGS efficacy within the PulseNet framework for improving outbreak detection and response.

Main Methods:

  • Analysis of 743 Cronobacter isolates from clinical, food, and environmental sources.
  • Comparison of WGS subtyping methods: 7-gene MLST, cgMLST, wgMLST, and high-quality single nucleotide polymorphism (hqSNP) analysis.
  • Validation of WGS approaches against epidemiological data and hqSNP analysis.

Main Results:

  • cgMLST and wgMLST accurately identified closely related isolates and aligned with epidemiological findings.
  • Allele-based WGS analyses demonstrated comparable performance to hqSNP analysis.
  • The developed workflow provides 7-gene MLST allele calls, sequence types, and clonal complexes for historical comparisons.

Conclusions:

  • WGS-based approaches, specifically cgMLST and wgMLST, are effective for Cronobacter subtyping and surveillance.
  • These methods enhance outbreak detection and response, supporting public health efforts to prevent infant infections.
  • Implementation of cgMLST is recommended for routine PulseNet surveillance, with wgMLST and hqSNP offering higher resolution for investigations.

Keywords:
Cronobacter sakazakiicgMLSThqSNPinfant meningitispowdered infant formulawgMLST

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