Gmeiner, A.; Ivanova, M.; Njage, P. M. K.; Hansen, L. T.; Chindelevitch, L.; Leekitcharoenphon, P.

Listeria monocytogenes is a potentially severe disease-causing bacteria mainly transmitted through food. This pathogen is of great concern for public health and the food industry in particular. Many countries have implemented thorough regulations, and some have even set zero-tolerance thresholds for particular food products to minimise the risk of L. monocytogenes outbreaks. This emphasises that proper sanitation of food processing plants is of utmost importance. However, in recent years, there has been an increased reporting of L. monocytogenes tolerance to disinfectants used in the food industry. Even though many studies are focusing on laboratory quantification of L. monocytogenes tolerance, the possibility of predictive models remains poorly studied. Within this study, we explore the prediction of tolerance and minimum inhibitory concentrations (MIC) using whole genome sequencing (WGS) and machine learning (ML). We used 1649 L. monocytogenes WGS samples and their respective tolerance phenotypes to quaternary ammonium compound (QAC) disinfectants to train different ML predictors. Our study shows promising results for predicting tolerance to QAC disinfectants using WGS and machine learning. We were able to train high-performing ML classifiers to predict tolerance with balanced accuracy scores up to 0.97{+/-}0.02. For the prediction of MIC values, we were able to train ML regressors with mean squared error as low as 0.07{+/-}0.02. We also identified several new genes putatively associated with disinfectant tolerance in L. monocytogenes. The findings of this study are a first step towards tolerance prediction of L. monocytogenes to QAC disinfectants used in the food industry. In the future, predictive models might be used to monitor disinfectant tolerance in food production and might support the conceptualisation of more nuanced sanitation programs.