Genomic Characterization of Listeria innocua Isolates Recovered from Cattle Farms, Beef Abattoirs, and Retail Outlets in Gauteng Province, South Africa

Abstract

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.

A comparative study on the occurrence, genetic characteristics, and factors associated with the distribution of Listeria species on cattle farms and beef abattoirs in Gauteng Province, South Africa

“…In our study, L. innocua was detected with a higher farm prevalence than L. monocytogenes (11.3% versus 3.4%) and from each sample type (faeces, feeds, silage, and drinking water) collected from cattle farms in our study. These findings agree with published reports that L. innocua has a broader distribution on cattle farms elsewhere (Gradovska et al 2023 ; Gana et al 2023 ). However, considering the organism is viewed as a non-pathogen, the risk of causing livestock and human listeriosis is minimal.…”

Genomic Characterization of <em>Listeria innocua</em> Isolates Recovered from Cattle Farms, Beef Abattoirs, and Retail Outlets in Gauteng Province, South Africa

“…Therefore, there is a potential for tetracycline-resistant L. innocua strains to enter the human food chain. It is relevant to mention that the prevalence of phenotypic tetracycline resistance exhibited by the same isolates of L. innocua using the disc diffusion method was 36.8% [37]. Interestingly, this phenotypic resistance correlates well with the putative resistance to tetracycline due to both the tet(M) and tet(S) genes, suggesting that the genes may have been partly responsible for the resistance detected.…”

“…This is attributed to the existing Fertilizers, Farm, and Agricultural and Stock Remedy Act (Act 36, 1947), which legalizes the use of certain antimicrobial agents, such as sulphonamides and trimethoprim, to be purchased over-the-counter, and they are used for treatment and as growth promoters [70]. Interestingly, the phenotypic resistance exhibited to tetracycline (36.8%) determined by Gana [37] correlates well with the putative resistance to tetracycline due to both tet(M) and tet(S) genes based on WGS on the same isolates, suggesting that the genes may have been partly responsible for the resistance detected. Other studies have similarly reported the correlation between phenotypic resistance and the carriage of corresponding encoding resistance genes [65,71,72].…”

“…The isolates of L. innocua subjected to WGS in the current study originated from an earlier study. Details on the types and number of samples collected from the sources mentioned earlier and the types of samples in the current study have been documented [37].…”

Whole Genome Sequence Analysis of <em>Listeria monocytogenes</em> Isolates Recovered from Cattle Farms, Cattle Abattoirs, and Retail Outlets in Gauteng Province, South Africa

“…obtained from beef processing environments [40] and the red meat and poultry value chain [55]. Most recently, Gana et al [56] used WGS to characterize L. innocua isolates from cattle farms, abattoirs, and retail outlets. To date, there is a dearth of comprehensive information on the WGS analysis of L. monocytogenes circulating in the beef production chain's three levels (production, processing, and retailing) in Gauteng province, South Africa.…”