Genomic pitfalls in hospital surveillance: unexpected Enterobacter cloacae clustering without epidemiological link highlights the need for cautious core genome MLST analysis interpretation.

ABSTRACT: Whole-genome sequencing has become a key tool for identifying bacterial cross-transmission in healthcare settings. Among the methods used, core-genome Multi-Locus Sequence Typing (cgMLST) is considered as the reference method owing to its standardization. However, its limitations are often overlooked, particularly for taxonomically complex species such as Enterobacter cloacae. We report a case of false-positive genomic linkage between two E. cloacae isolates recovered from patients hospitalized in different units, four months apart, with no epidemiological overlap. Routine retrospective genomic surveillance using a local cgMLST scheme flagged these isolates as genetically related. However, further analyses based on core-genome Single-Nucleotide Polymorphism (SNPs) calling and molecular phy

SUBMITTER: Danjean M 

PROVIDER: S-EPMC12746620 | biostudies-literature | 2025 Dec

REPOSITORIES: biostudies-literature