Molecular typing and genomic characterization of persistent Listeria monocytogenes clones in a bakery production...

Listeria monocytogenes is a foodborne pathogen and the leading cause of hospitalization and death resulting from the consumption of contaminated food. Its ability to survive and multiply under adverse conditions requires targeted monitoring by the food industry. Molecular typing techniques have been used to characterize isolates and to identify persistent clones. Nowadays, whole genome sequencing (WGS) provides unprecedented resolution for subtyping, allowing the identification of facility-specific molecular signatures and genetic elements that may contribute to persistence. The aim of this study was to characterize L. monocytogenes isolates from a bakery industry combining Pulsed-Field Gel Electrophoresis (PFGE) and WGS to identify persistent clones and uncover genomic features that may underlie their ability to persist. In the present study, persistent clones were defined as the repeated isolation, over a period exceeding one year, of isolates belonging to the same cgMLST type from the production environment and/or final product. A total of 68 L. monocytogenes isolates were molecular serotyped, typed by PFGE and sequenced to determine Multilocus Sequence Typing (MLST) and core genome MLST types. Loci encoding genes associated with virulence, antibiotic resistance, metal and disinfectant resistance, stress response islands, Listeria genomic islands, and the sigB operon were assessed. These isolates were classified into three molecular serotypes: IIb, IIc, and IVb, into 17 distinct PFGE types and 10 cgMLST types. The results showed the existence of two persistent clones belonging to CC2 and CC9 accounting for 86% of the isolates. Cheese could be the source of CC9, while it was not possible to identify the source of CC2 isolates. Relevant genetic features were identified; however, persistence could not be conclusively linked to specific genomic determinants.