Gana, JamesGcebe, NomakorintePierneef, Rian EwaldChen, YiMoerane, ReboneAdesiyun, Abiodun Adewale2024-09-062024-09-062023-08-18Gana, J.; Gcebe, N.; Pierneef, R.E.; Chen, Y.; Moerane, R.; Adesiyun, A.A. Genomic Characterization of Listeria innocua Isolates Recovered from Cattle Farms, Beef Abattoirs, and Retail Outlets in Gauteng Province, South Africa. Pathogens 2023, 12, 1062. https://DOI.org/10.3390/pathogens12081062.2076-0817 (online)10.3390/pathogens12081062http://hdl.handle.net/2263/98063DATA AVAILABILITY STATEMENT : All samples have been deposited under NCBI BioProject: PRJNA215355 and can be searched based on the isolate CFSAN identifier.SUPPLEMENTARY MATERIALS : TABLE S1. Coverage of the sequences used in the study, TABLE S2. Sources, types of samples, sequence types, and resistance genes detected in 110 L. innocua, TABLE S3. Sources, types of samples, sequence types, and virulence genes detected in L. innocua isolates, TABLE S4. Sequence Type (ST) profiles and associated loci, TABLE S5. Sources, types of samples, sequence types, phenotypic AMR, and genomic AMR profiles, types of samples, sequence types, phenotypic AMR and genomic AMR profiles.Whole-genome sequencing (WGS) was used for the genomic characterization of one hundred and ten strains of Listeria innocua (L. innocua) isolated from twenty-three cattle farms, eight beef abattoirs, and forty-eight retail outlets in Gauteng province, South Africa. In silico multilocus sequence typing (MLST) was used to identify the isolates' sequence types (STs). BLAST-based analyses were used to identify antimicrobial and virulence genes. The study also linked the detection of the genes to the origin (industries and types of samples) of the L. innocua isolates. The study detected 14 STs, 13 resistance genes, and 23 virulence genes. Of the 14 STs detected, ST637 (26.4%), ST448 (20%), 537 (13.6%), and 1085 (12.7%) were predominant, and the frequency varied significantly (p < 0.05). All 110 isolates of L. innocua were carriers of one or more antimicrobial resistance genes, with resistance genes lin (100%), fosX (100%), and tet(M) (30%) being the most frequently detected (p < 0.05). Of the 23 virulence genes recognized, 13 (clpC, clpE, clpP, hbp1, svpA, hbp2, iap/cwhA, lap, lpeA, lplA1, lspA, oatA, pdgA, and prsA2) were found in all 110 isolates of L. innocua. Overall, diversity and significant differences were detected in the frequencies of STs, resistance, and virulence genes according to the origins (source and sample type) of the L. innocua isolates. This, being the first genomic characterization of L. innocua recovered from the three levels/industries (farm, abattoir, and retail) of the beef production system in South Africa, provides data on the organism's distribution and potential food safety implications.en© 2023 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license.Listeria innocuaSouth Africa (SA)Antimicrobial resistance genes (ARGs)Beef production chainSequence typeVirulence genesWhole-genome sequencing (WGS)Multilocus sequence typing (MLST)SDG-02: Zero hungerSDG-03: Good health and well-beingArticle