Genomic characterisation of Listeria monocytogenes isolated from normally sterile human body fluids in Lithuania from 2016 to 2021

Listeria monocytogenes is a saprophytic gram positive bacterium and opportunistic foodborne pathogen that can cause listeriosis in humans. The incidence of listeriosis has been rising globally and, despite antimicrobial treatment, the mortality rates associated with the most severe forms of listeriosis such as sepsis, meningitis, and meningoencephalitis remain high. The notification of listeriosis in humans is mandatory in Lithuania and up to 10 cases are reported annually. However, no studies have described the detailed virulence and antimicrobial susceptibility profiles of any clinical L. monocytogenes strains in Lithuania. Accordingly, this study aimed to describe the antibiotic susceptibility of invasive L. monocytogenes and perform in-depth characterisation of strains isolated from patients with neuroinfections through whole-genome sequencing. A total of 70 isolates were collected, mostly from infected patients aged 65 or older, between 2016 and 2021: 41 (58.6%) from blood, 19 (27.1%) from cerebrospinal fluid, five (7.1%) from wounds, one (1.4%) from pleural fluid, and one (1.4%) from a brain abscess. Two phylogenetic lineages were identified--I (n = 16/70, 22.9%) and II (n = 54/70, 77.1%)--along with three serogroups--IIa (n = 53/70, 75.7%), IVb (n = 16/70, 22.9%), and IIc (n = 1/70, 1.4%). Genomic analysis of 20 isolates showed a high level of diversity with seven genotypes: ST6 (n = 6), ST155 (n = 5), ST8 (n = 4), ST504 (n = 2), and singletons for ST37, ST451, and ST2. Phylogenetic analysis clustered these isolates into two clades defined by serogroups IVb and IIa. Notably, five isolates were clustered tightly together (difference of 6-48 core SNPs from reference and 0, 4, or 44 SNPs from each other) with ST155, previously reported in a European outbreak. Comparison with publicly available L. monocytogenes genomes did not identify unique clusters or genotypes. No acquired antimicrobial resistance genes were identified. Our study highlights the complementary value of whole-genome sequencing in routine PCR-based surveillance in Lithuania. This is the first study to characterise and compare genomes for L. monocytogenes associated with neuroinfections in Lithuania using whole-genome sequencing. The retrospective detection of the ST155 clone underscores the need for a review and strengthening of epidemiological surveillance strategies in clinical and non-clinical settings in Lithuania. Data summaryThe raw sequencing reads from the L. monocytogenes isolates generated in this study are available from the European Nucleotide Archive (https://www.ebi.ac.uk/ena/browser/home) under project accession number PRJEB80562; accession numbers for individual isolates are provided in Suppl. Table S1. Draft genomes of the L. monocytogenes strains were submitted to the BIGSdb-Lm database (https://bigsdb.pasteur.fr/listeria/) under accession numbers 110263-110281 and 108726.