Exploration of the biodiversity and mining novel target genes of Listeria monocytogenes strains isolated from beef through comparative genomics analysis

<i>L. monocytogenes</i> is a significant foodborne pathogen. This study aims to explore the biodiversity and evolutionary characteristics of <i>L. monocytogenes</i> isolated from beef through pan-genome analysis, and to provide important reference value for its specific molecular detection. This study conducted an in-depth analysis of the virulence genes, antimicrobial resistance genes, and environmental resistance genes of 344 <i>L. monocytogenes</i> strains isolated from beef. Pan-genomic analysis revealed that <i>L. monocytogenes</i> from beef have open genomes, providing a solid genetic basis for adaptation to different environments. MLST analysis revealed that the most prevalent types of <i>L. monocytogenes</i> isolated from beef were ST9 and CC9. A total of 50 virulence genes were detected in these strains, with 26 virulence genes such as <i>inlA</i>, <i>inlB</i>, <i>plcA</i>, <i>plcB</i>, and <i>prfA</i>, present in all <i>L. monocytogenes</i> strains. The four most prevalent antibiotic resistance genes in <i>L. monocytogenes</i> were <i>norB</i>, <i>lin</i>, <i>mprF</i>, and <i>FosX</i>, indicating high resistance to fluoroquinolones, lincosamides, peptides, and phosphonic acid antibiotics. A total of 416 potential target genes were identified through pan-genomic screening, which were then further filtered using a hub gene selection method to mining novel target genes. Ultimately, 10 highly connected hub genes were selected: <i>bglF_2</i>, <i>tilS</i>, <i>group_2105</i>, <i>group_2431</i>, <i>oleD</i>, <i>ndk</i>, <i>flgG</i>, <i>purB</i>, <i>pbpB</i>, and <i>fni</i>. These genes play a crucial role in the pathogenesis of <i>L. monocytogenes</i>. The PCR results demonstrated the excellent specificity of the <i>bglF_2</i> gene for <i>L. monocytogenes</i>. Moreover, in the artificial contamination experiment, the <i>bglF_2</i> gene was able to effectively detect <i>L. monocytogenes</i> in beef samples. Therefore, the <i>bglF_2</i> gene holds potential as a specific molecular target for the detection of <i>L. monocytogenes</i> strains in beef samples.