Predicting Antibiotic Resistance in Listeria monocytogenes from Food and Food-Processing Environments Using Next-Generation Sequencing: A Systematic Review
Abstract
Listeria monocytogenes is a ubiquitous foodborne pathogen whose occurrence in food and food-processing environments raises public-health concerns, particularly when isolates carry antimicrobial-resistance determinants. Next-generation sequencing (NGS) is increasingly used to detect resistance genes and to predict phenotypic resistance. Following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA 2020) guidelines, PubMed, Web of Science, and Scopus were searched for original articles (2015-2024) that used second- and/or third-generation sequencing to characterize antibiotic resistance in L. monocytogenes from food and food-processing environments. After deduplication and screening, 58 studies were included from an initial 418 records. NGS reliably detected a set of recurrent resistance determinants across diverse sample types and geographies. The fosX locus (intrinsic fosfomycin-related marker) was effectively ubiquitous across studies, while acquired determinants were variably distributed: lin (35/58 studies, 60.34%), norB (33/58, 56.90%), and tetracycline genes overall in 20/58 (34.48%) with tetM as the most common (11/58, 18.97%). Reported concordance between the genotypes and phenotypes for acquired resistance was very high (>99% for most agents), with notable exceptions (e.g., ciprofloxacin and some fosfomycin cases). Common analysis pipelines and databases included ResFinder, CARD, BIGSdb-Lm, ABRicate, and ARIBA; most sequencing used Illumina…
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