PP 15 - Genetic diversity and clonal relationships of clinical Listeria monocytogenes isolates in Sri Lankae sequencing

Pathirage S, Kaushalya RH, Arachchige NDS, Sandeepani SAN, Sandeepani LAD, Gunathilaka HMGU  , Medical Research Institute, Colombo 08

Abstract

Introduction

Listeria monocytogenes is a facultative intracellular pathogen of major public health significance. However genomic characterization of L. monocytogenes in Sri Lanka has not been well elucidated, which is crucial for effective surveillance and control strategies.

Objective

This study aimed to determine the genetic diversity and clonal relatedness of clinical  L. monocytogenes isolates using whole genome sequencing.

Design, setting, and methods

A retrospective laboratory based descriptive study was conducted at the Medical Research Institute (MRI), Colombo 08, Sri Lanka. The study utilised blood isolates (n=6) received at the MRI in the year 2025 from hospitalised patients suspected of Listeriosis. Isolates were initially identified as L. monocytogenes by an automated microbiology analyser (The BD Phoenix™ M50). DNA was extracted (DNeasy Blood & Tissue Kits) and the DNA library was prepared (SQK-RBK110.96) for whole genome sequencing using Oxford Nanopore Technologies sequencer (MinION Mk1D) and FLO-MIN114 flowcell. Resulting sequences were basecalled by Dorado software with Q-score threshold of Q10. Genomes were de novo assembled using FLYE software. Antimicrobial Resistant (AMR) gene profiles and Sequence Types (STs) were defined via AbriTAMR and MLST tools.

Results

All the isolates were confirmed as L. monocytogenes. Two sequence types were identified. One clinical isolate was ST1, belonging to the globally distributed clinically dominant clone. Five clinical isolates (n=5) were ST308. Both the STs had common serotypes 4b, 4d, and 4e that form a distinct genomic cluster (IIB). ST1 differed from ST 308 by a mutation at D-amino acid aminotransferase (dat) housekeeping gene.  All six isolates had fosX and vga(G) genes that represent resistance to fosfomycin and lincosamides respectively.

Conclusions

ST308 emerges as a predominant clinical sequence type among the L. monocytogenes isolates evaluated, alongside the globally significant ST1 clone. These findings provide a crucial genomic baseline for Sri Lanka and emphasize the need to expand sequencing efforts into food and environmental sectors to effectively monitor and control Listeriosis.