Abstract:
The study used whole-genome sequencing (WGS) and bioinformatics analysis for the
genomic characterization of 60 isolates of Listeria monocytogenes obtained from the beef production
chain (cattle farms, abattoirs, and retail outlets) in Gauteng province, South Africa. The sequence
types (STs), clonal complexes (CCs), and the lineages of the isolates were determined using in
silico multilocus sequence typing (MLST). We used BLAST-based analyses to identify virulence
and antimicrobial genes, plasmids, proviruses/prophages, and the CRISPR-Cas system. The study
investigated any association of the detected genes to the origin in the beef production chain of the
L. monocytogenes isolates. Overall, in 60 isolates of Listeria monocytogenes, there were seven STs, six CCs,
forty-four putative virulence factors, two resistance genes, one plasmid with AMR genes, and three
with conjugative genes, one CRISPR gene, and all 60 isolates were positive for proviruses/prophages.
Among the seven STs detected, ST204 (46.7%) and ST2 (21.7%) were the most prominent, with ST
frequency varying significantly (p < 0.001). The predominant CC detected were CC2 (21.7%) and
CC204 (46.7%) in lineages I and II, respectively. Of the 44 virulence factors detected, 26 (across Listeria
Pathogenicity Islands, LIPIs) were present in all the isolates. The difference in the detection frequency
varied significantly (p < 0.001). The two AMR genes (fosX and vga(G)) detected were present in all
60 (100%) isolates of L. monocytogenes. The only plasmid, NF033156, was present in three (5%) isolates.
A CRISPR-Cas system was detected in six (10%), and all the isolates carried proviruses/prophages.
The source and sample type significantly affected the frequencies of STs and virulence factors in the
isolates of L. monocytogenes. The presence of fosX and vga(G) genes in all L. monocytogenes isolates
obtained from the three industries of the beef production chain can potentially cause therapeutic
implications. Our study, which characterized L. monocytogenes recovered from the three levels in the
beef production chain, is the first time genomics was performed on this type of data set in the country,
and this provides insights into the health implications of Listeria.
Description:
DATA AVAILABILITY STATEMENT : All samples have been deposited under NCBI BioProject PRJNA215355
and can be searched based on the isolated CFSAN identifier.
SUPPLEMENTARY MATERIALS : SUPPLEMENTARY TABLE S1. Coverage of the sequences used for further analysis; SUPPLEMENTARY TABLE S2. Sample Information: Source and Type of sample, ST and CC of isolates; SUPPLEMENTARY TABLE S3. Distribution of clonal complexes and lineages in 60 L. monocytogenes recovered from cattle farms, abattoirs, and retail outlets in Gauteng province; SUPPLEMENTARY TABLE S4. Virulence factors; SUPPLEMENTARY TABLE S5. AMR data; SUPPLEMENTARY TABLE S6. AMR and Conjugative plasmid genes; SUPPLEMENTARY TABLE S7. Provirus; SUPPLEMENTARY TABLE S8. CRISPR; SUPPLEMENTARY TABLE S9. Type and frequency of virulence factors detected according to the industries. References [29,101,117] are cited in the Supplementary Materials.
