A novel metagenomic approach uncovers phage genes as markers for increased disinfectant tolerance in mixed Listeria monocytogenes communities
Listeria monocytogenes is an important human pathogen with high mortality rate. Consumption of contaminated during production ready-to-eat food is the main mode of transmission to humans. Disinfectant-tolerant L. monocytogenes strains have emerged, which is believed to increase their persistence potential. Elucidating the mechanisms of L. monocytogenes disinfectant tolerance has been the focus of previous studies using pure cultures. A limitation of this approach is the difficulty to identify strains with reduced susceptibility due to inter-strain variation and the need to screen large numbers of strains and genes. In this study, we applied a novel metagenomic approach to detect disinfectant-associated genes in mixed L. monocytogenes planktonic communities. Two communities, consisting of 71 and 80 isolates each, were treated with the food industry disinfectants benzalkonium chloride (BC, 1.75 mg/L) and peracetic acid (PAA, 38 mg/L). The communities were metagenomically sequenced and differences in individual gene abundances between biocide-free control communities and biocide-treated communities were investigated. A significant increase in the abundance of Listeria phage-associated genes was observed in both communities after treatment, suggesting that prophage harborage could lead to an increased disinfectant tolerance in mixed L. monocytogenes planktonic communities. In opposite, a significant decrease in the abundance of the high-copy emrC-harbouring plasmid pLmN12-0935 was observed in both communities after treatment. For PAA, a putative ABC transporter previously found to be necessary for L. monocytogenes resistance to antimicrobial agents and virulence, was among the genes that had highest weight for differentiating treatment from control samples.